15-39774154-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.126+2245G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,040 control chromosomes in the GnomAD database, including 1,834 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 0.12 (1834 hom., cov: 32)
• Consequence: FSIP1 NM_152597.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105

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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FSIP1	NM_152597.5	c.126+2245G>A		intron_variant		ENST00000350221.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FSIP1	ENST00000350221.4	c.126+2245G>A		intron_variant		1	NM_152597.5	P1

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18888 AN: 151922 Hom.: 1838 Cov.: 32

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0781

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.0642

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0496

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.124 AC: 18898 AN: 152040 Hom.: 1834 Cov.: 32 AF XY: 0.125 AC XY: 9258 AN XY: 74306

Gnomad4 AFR AF: 0.261

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.0781

Gnomad4 EAS AF: 0.248

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.0642

Gnomad4 NFE AF: 0.0496

Gnomad4 OTH AF: 0.115

Alfa AF: 0.0909 Hom.: 175

Bravo AF: 0.133

Asia WGS AF: 0.167 AC: 582 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	10
Dann	Benign	0.76

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: rs1602543; hg19: chr15-40066355;