15-39770624-C-T

Position:

• chr15-39770624-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.127-14G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 1,378,010 control chromosomes in the GnomAD database, including 8,653 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 0.11 (1009 hom., cov: 32)
  • Exomes 𝑓: 0.11 (7644 hom.)
• Consequence: FSIP1 NM_152597.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680

Genes affected

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

ENSG00000259580 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.124 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FSIP1	NM_152597.5	c.127-14G>A		intron_variant		ENST00000350221.4	NP_689810.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FSIP1	ENST00000350221.4	c.127-14G>A		intron_variant		1	NM_152597.5	ENSP00000280236.3
ENSG00000259580	ENST00000558616.1	n.267-14G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.112 AC: 16763 AN: 149050 Hom.: 1013 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.0642

Gnomad AMR AF: 0.0778

Gnomad ASJ AF: 0.0877

Gnomad EAS AF: 0.000392

Gnomad SAS AF: 0.0704

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.0701

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.114

GnomAD3 exomes AF: 0.111 AC: 14106 AN: 127340 Hom.: 786 AF XY: 0.113 AC XY: 7862 AN XY: 69678

Gnomad AFR exome AF: 0.155

Gnomad AMR exome AF: 0.0604

Gnomad ASJ exome AF: 0.103

Gnomad EAS exome AF: 0.000632

Gnomad SAS exome AF: 0.0850

Gnomad FIN exome AF: 0.122

Gnomad NFE exome AF: 0.129

Gnomad OTH exome AF: 0.106

GnomAD4 exome AF: 0.112 AC: 137918 AN: 1228854 Hom.: 7644 Cov.: 22 AF XY: 0.111 AC XY: 67056 AN XY: 601438

Gnomad4 AFR exome AF: 0.126

Gnomad4 AMR exome AF: 0.0653

Gnomad4 ASJ exome AF: 0.0867

Gnomad4 EAS exome AF: 0.000277

Gnomad4 SAS exome AF: 0.0697

Gnomad4 FIN exome AF: 0.115

Gnomad4 NFE exome AF: 0.120

Gnomad4 OTH exome AF: 0.103

GnomAD4 genome AF: 0.112 AC: 16755 AN: 149156 Hom.: 1009 Cov.: 32 AF XY: 0.108 AC XY: 7887 AN XY: 72854

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.0776

Gnomad4 ASJ AF: 0.0877

Gnomad4 EAS AF: 0.000393

Gnomad4 SAS AF: 0.0695

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.112

Alfa AF: 0.0713 Hom.: 338

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	2.5
DANN	Benign	0.72

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: rs1565560; hg19: chr15-40062825;