chr15-39747694-C-T

Variant names:

• chr15-39747694-C-T
• rs7179417
• NM_152597.5:c.560-5794G>A

Variant summary

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

The NM_152597.5(FSIP1):​c.560-5794G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.587 in 151,990 control chromosomes in the GnomAD database, including 26,725 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 0.59 (26725 hom., cov: 32)
• Consequence: FSIP1 NM_152597.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• 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 (AFR) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FSIP1	NM_152597.5	c.560-5794G>A		intron_variant	Intron 5 of 11	ENST00000350221.4	NP_689810.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FSIP1	ENST00000350221.4	c.560-5794G>A		intron_variant	Intron 5 of 11	1	NM_152597.5	ENSP00000280236.3
FSIP1	ENST00000559692.1	n.-247G>A		upstream_gene_variant		3

Frequencies

GnomAD3 genomes AF: 0.587 AC: 89142 AN: 151870 Hom.: 26702 Cov.: 32

Gnomad AFR AF: 0.692

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.563

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

GnomAD4 genome AF: 0.587 AC: 89219 AN: 151990 Hom.: 26725 Cov.: 32 AF XY: 0.586 AC XY: 43549 AN XY: 74302

African (AFR) AF: 0.692 AC: 28687 AN: 41476

American (AMR) AF: 0.619 AC: 9446 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1634 AN: 3466

East Asian (EAS) AF: 0.481 AC: 2489 AN: 5178

South Asian (SAS) AF: 0.426 AC: 2057 AN: 4824

European-Finnish (FIN) AF: 0.619 AC: 6537 AN: 10562

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.540 AC: 36643 AN: 67914

Other (OTH) AF: 0.564 AC: 1191 AN: 2110

Alfa AF: 0.557 Hom.: 63554

Bravo AF: 0.595

Asia WGS AF: 0.488 AC: 1696 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.98
DANN	Benign	0.23
PhyloP100		-1.2
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: rs7179417; hg19: chr15-40039895;