15-39766212-A-G

Variant names:

• chr15-39766212-A-G
• rs2576932
• NM_152597.5:c.311-466T>C

Variant summary

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

The NM_152597.5(FSIP1):​c.311-466T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.578 in 152,040 control chromosomes in the GnomAD database, including 25,861 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 0.58 (25861 hom., cov: 32)
• Consequence: FSIP1 NM_152597.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.783
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.658 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FSIP1	NM_152597.5	MANE Select	c.311-466T>C		intron	N/A	NP_689810.3
	FSIP1	NM_001324338.2		c.311-466T>C		intron	N/A	NP_001311267.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FSIP1	ENST00000350221.4	TSL:1 MANE Select	c.311-466T>C		intron	N/A	ENSP00000280236.3

Frequencies

GnomAD3 genomes AF: 0.578 AC: 87828 AN: 151920 Hom.: 25831 Cov.: 32

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.578 AC: 87916 AN: 152040 Hom.: 25861 Cov.: 32 AF XY: 0.577 AC XY: 42897 AN XY: 74294

African (AFR) AF: 0.664 AC: 27555 AN: 41484

American (AMR) AF: 0.617 AC: 9434 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1633 AN: 3466

East Asian (EAS) AF: 0.484 AC: 2510 AN: 5186

South Asian (SAS) AF: 0.427 AC: 2059 AN: 4826

European-Finnish (FIN) AF: 0.606 AC: 6387 AN: 10542

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.539 AC: 36627 AN: 67946

Other (OTH) AF: 0.560 AC: 1180 AN: 2108

Alfa AF: 0.467 Hom.: 1658

Bravo AF: 0.587

Asia WGS AF: 0.495 AC: 1721 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.45
DANN	Benign	0.62
PhyloP100		-0.78
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: rs2576932; hg19: chr15-40058413;