chr15-39767334-G-A

Variant names:

• chr15-39767334-G-A
• rs12440567
• NM_152597.5:c.311-1588C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152597.5(FSIP1):​c.311-1588C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 152,100 control chromosomes in the GnomAD database, including 1,797 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.14 (1797 hom., cov: 32)
• Consequence: FSIP1 NM_152597.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.93
• Publications: 3 publications found

Genes affected

FSIP1 (HGNC:21674): (fibrous sheath interacting protein 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152597.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FSIP1	NM_152597.5	MANE Select	c.311-1588C>T		intron	N/A	NP_689810.3
	FSIP1	NM_001324338.2		c.311-1588C>T		intron	N/A	NP_001311267.1	Q8NA03

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FSIP1	ENST00000350221.4	TSL:1 MANE Select	c.311-1588C>T		intron	N/A	ENSP00000280236.3	Q8NA03
	FSIP1	ENST00000884361.1		c.311-1588C>T		intron	N/A	ENSP00000554420.1
	FSIP1	ENST00000942556.1		c.311-1588C>T		intron	N/A	ENSP00000612615.1

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20946 AN: 151980 Hom.: 1791 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.0867

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.147

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.138 AC: 20965 AN: 152100 Hom.: 1797 Cov.: 32 AF XY: 0.143 AC XY: 10614 AN XY: 74354

African (AFR) AF: 0.129 AC: 5369 AN: 41460

American (AMR) AF: 0.266 AC: 4067 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0867 AC: 301 AN: 3472

East Asian (EAS) AF: 0.202 AC: 1045 AN: 5180

South Asian (SAS) AF: 0.141 AC: 680 AN: 4808

European-Finnish (FIN) AF: 0.177 AC: 1869 AN: 10576

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7231 AN: 68000

Other (OTH) AF: 0.145 AC: 307 AN: 2112

Alfa AF: 0.148 Hom.: 404

Bravo AF: 0.146

Asia WGS AF: 0.200 AC: 695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	7.9
DANN	Benign	0.74
PhyloP100		1.9
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: rs12440567; hg19: chr15-40059535;