15-81309441-T-C

Variant names:

• chr15-81309441-T-C
• rs1131445
• NM_172217.5:c.*643T>C

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_172217.5(IL16):​c.*643T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 152,618 control chromosomes in the GnomAD database, including 8,026 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.32 (7995 hom., cov: 33)
  • Exomes 𝑓: 0.33 (31 hom.)
• Consequence: IL16 NM_172217.5 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.375
• Publications: 55 publications found

Genes affected

IL16 (HGNC:5980): (interleukin 16) The protein encoded by this gene is a pleiotropic cytokine that functions as a chemoattractant, a modulator of T cell activation, and an inhibitor of HIV replication. The signaling process of this cytokine is mediated by CD4. The product of this gene undergoes proteolytic processing, which is found to yield two functional proteins. The cytokine function is exclusively attributed to the secreted C-terminal peptide, while the N-terminal product may play a role in cell cycle control. Caspase 3 is reported to be involved in the proteolytic processing of this protein. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Feb 2010]

STARD5 (HGNC:18065): (StAR related lipid transfer domain containing 5) Proteins containing a steroidogenic acute regulatory-related lipid transfer (START) domain are often involved in the trafficking of lipids and cholesterol between diverse intracellular membranes. This gene is a member of the StarD subfamily that encodes START-related lipid transfer proteins. The protein encoded by this gene is a cholesterol transporter and is also able to bind and transport other sterol-derived molecules related to the cholesterol/bile acid biosynthetic pathways such as 25-hydroxycholesterol. Its expression is upregulated during endoplasmic reticulum (ER) stress. The protein is thought to act as a cytosolic sterol transporter that moves cholesterol between intracellular membranes such as from the cytoplasm to the ER and from the ER to the Golgi apparatus. Alternative splicing of this gene produces multiple transcript variants. [provided by RefSeq, Jan 2016]

ENSG00000271725 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 15-81309441-T-C is Benign according to our data. Variant chr15-81309441-T-C is described in ClinVar as Benign. ClinVar VariationId is 1261119.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_172217.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL16	NM_172217.5	MANE Select	c.*643T>C		3_prime_UTR	Exon 19 of 19	NP_757366.2
	STARD5	NM_181900.3	MANE Select	c.*3815A>G		3_prime_UTR	Exon 6 of 6	NP_871629.1
	STARD5	NR_135013.2		n.4449A>G		non_coding_transcript_exon	Exon 5 of 5

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL16	ENST00000683961.1	MANE Select	c.*643T>C		3_prime_UTR	Exon 19 of 19	ENSP00000508085.1
	STARD5	ENST00000302824.7	TSL:1 MANE Select	c.*3815A>G		3_prime_UTR	Exon 6 of 6	ENSP00000304032.6
	IL16	ENST00000302987.10	TSL:1	c.*643T>C		3_prime_UTR	Exon 19 of 19	ENSP00000302935.5

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48992 AN: 151996 Hom.: 7984 Cov.: 33

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.345

GnomAD4 exome AF: 0.329 AC: 165 AN: 502 Hom.: 31 Cov.: 0 AF XY: 0.317 AC XY: 90 AN XY: 284

African (AFR) AF: 0.250 AC: 2 AN: 8

American (AMR) AF: 0.200 AC: 2 AN: 10

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 3 AN: 18

East Asian (EAS) AF: 0.172 AC: 11 AN: 64

South Asian (SAS) AF: 0.00 AC: 0 AN: 6

European-Finnish (FIN) AF: 0.327 AC: 17 AN: 52

Middle Eastern (MID) AF: 0.500 AC: 2 AN: 4

European-Non Finnish (NFE) AF: 0.377 AC: 120 AN: 318

Other (OTH) AF: 0.364 AC: 8 AN: 22

GnomAD4 genome AF: 0.322 AC: 49045 AN: 152116 Hom.: 7995 Cov.: 33 AF XY: 0.318 AC XY: 23630 AN XY: 74376

African (AFR) AF: 0.303 AC: 12554 AN: 41488

American (AMR) AF: 0.257 AC: 3929 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1413 AN: 3470

East Asian (EAS) AF: 0.311 AC: 1609 AN: 5170

South Asian (SAS) AF: 0.237 AC: 1144 AN: 4828

European-Finnish (FIN) AF: 0.329 AC: 3474 AN: 10570

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.349 AC: 23724 AN: 67980

Other (OTH) AF: 0.351 AC: 740 AN: 2108

Alfa AF: 0.334 Hom.: 14774

Bravo AF: 0.317

Asia WGS AF: 0.298 AC: 1037 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

Jul 15, 2020

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 24465869)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.7
DANN	Benign	0.71
PhyloP100		0.38
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1131445; hg19: chr15-81601782;