rs1565560

Variant names:

• chr15-39770624-C-A
• rs1565560
• NM_152597.5:c.127-14G>T

Your query was ambiguous. Multiple possible variants found:

• chr15-39770624-C-A
• chr15-39770624-C-T

Variant summary

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

The NM_152597.5(FSIP1):​c.127-14G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 1,373,862 control chromosomes in the GnomAD database, including 82,689 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.30 (7717 hom., cov: 32)
  • Exomes 𝑓: 0.35 (74972 hom.)
• Consequence: FSIP1 NM_152597.5 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.0680
• Publications: 4 publications found

Genes affected

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

ENSG00000259580 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BP6: Variant 15-39770624-C-A is Benign according to our data. Variant chr15-39770624-C-A is described in ClinVar as Benign. ClinVar VariationId is 402884.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.413 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FSIP1	NM_152597.5	c.127-14G>T		intron_variant	Intron 2 of 11	ENST00000350221.4	NP_689810.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FSIP1	ENST00000350221.4	c.127-14G>T		intron_variant	Intron 2 of 11	1	NM_152597.5	ENSP00000280236.3
ENSG00000259580	ENST00000558616.1	n.267-14G>T		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.303 AC: 45172 AN: 149030 Hom.: 7707 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.301

GnomAD2 exomes AF: 0.386 AC: 49117 AN: 127340 AF XY: 0.388

Gnomad AFR exome AF: 0.150

Gnomad AMR exome AF: 0.537

Gnomad ASJ exome AF: 0.371

Gnomad EAS exome AF: 0.306

Gnomad FIN exome AF: 0.456

Gnomad NFE exome AF: 0.397

Gnomad OTH exome AF: 0.409

GnomAD4 exome AF: 0.355 AC: 434437 AN: 1224726 Hom.: 74972 Cov.: 22 AF XY: 0.353 AC XY: 211597 AN XY: 599420

African (AFR) AF: 0.113 AC: 2882 AN: 25450

American (AMR) AF: 0.493 AC: 10118 AN: 20542

Ashkenazi Jewish (ASJ) AF: 0.313 AC: 5843 AN: 18644

East Asian (EAS) AF: 0.299 AC: 9700 AN: 32398

South Asian (SAS) AF: 0.267 AC: 14424 AN: 54104

European-Finnish (FIN) AF: 0.431 AC: 19047 AN: 44212

Middle Eastern (MID) AF: 0.266 AC: 1314 AN: 4936

European-Non Finnish (NFE) AF: 0.363 AC: 354034 AN: 974728

Other (OTH) AF: 0.343 AC: 17075 AN: 49712

GnomAD4 genome AF: 0.303 AC: 45209 AN: 149136 Hom.: 7717 Cov.: 32 AF XY: 0.309 AC XY: 22524 AN XY: 72842

African (AFR) AF: 0.131 AC: 5244 AN: 40174

American (AMR) AF: 0.422 AC: 6360 AN: 15084

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1043 AN: 3430

East Asian (EAS) AF: 0.238 AC: 1209 AN: 5088

South Asian (SAS) AF: 0.265 AC: 1245 AN: 4706

European-Finnish (FIN) AF: 0.437 AC: 4421 AN: 10124

Middle Eastern (MID) AF: 0.236 AC: 69 AN: 292

European-Non Finnish (NFE) AF: 0.367 AC: 24665 AN: 67284

Other (OTH) AF: 0.304 AC: 628 AN: 2064

Alfa AF: 0.199 Hom.: 338

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:1

Mar 29, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

not provided Benign:1

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	2.1
DANN	Benign	0.69
PhyloP100		-0.068
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: rs1565560; hg19: chr15-40062825;