rs7179417

chr15-39747694-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
FSIP1	NM_152597.5	c.560-5794G>A		intron_variant		ENST00000350221.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FSIP1	ENST00000350221.4	c.560-5794G>A		intron_variant		1	NM_152597.5	P1

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

Gnomad4 AFR AF: 0.692

Gnomad4 AMR AF: 0.619

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.481

Gnomad4 SAS AF: 0.426

Gnomad4 FIN AF: 0.619

Gnomad4 NFE AF: 0.540

Gnomad4 OTH AF: 0.564

Alfa AF: 0.544 Hom.: 37199

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs7179417; hg19: chr15-40039895;