15-39770624-C-T

Variant names:

• chr15-39770624-C-T
• rs1565560
• NM_152597.5:c.127-14G>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.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
• Publications: 4 publications found

Genes affected

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

ENSG00000259580 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
FSIP1	NM_152597.5	c.127-14G>A		intron_variant	Intron 2 of 11	ENST00000350221.4	NP_689810.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FSIP1	ENST00000350221.4	c.127-14G>A		intron_variant	Intron 2 of 11	1	NM_152597.5	ENSP00000280236.3
ENSG00000259580	ENST00000558616.1	n.267-14G>A		intron_variant	Intron 2 of 2	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

GnomAD2 exomes AF: 0.111 AC: 14106 AN: 127340 AF XY: 0.113

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 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

African (AFR) AF: 0.126 AC: 3205 AN: 25412

American (AMR) AF: 0.0653 AC: 1348 AN: 20636

Ashkenazi Jewish (ASJ) AF: 0.0867 AC: 1620 AN: 18680

East Asian (EAS) AF: 0.000277 AC: 9 AN: 32480

South Asian (SAS) AF: 0.0697 AC: 3788 AN: 54336

European-Finnish (FIN) AF: 0.115 AC: 5115 AN: 44320

Middle Eastern (MID) AF: 0.0611 AC: 302 AN: 4946

European-Non Finnish (NFE) AF: 0.120 AC: 117412 AN: 978166

Other (OTH) AF: 0.103 AC: 5119 AN: 49878

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

African (AFR) AF: 0.127 AC: 5096 AN: 40168

American (AMR) AF: 0.0776 AC: 1171 AN: 15088

Ashkenazi Jewish (ASJ) AF: 0.0877 AC: 301 AN: 3432

East Asian (EAS) AF: 0.000393 AC: 2 AN: 5090

South Asian (SAS) AF: 0.0695 AC: 327 AN: 4706

European-Finnish (FIN) AF: 0.120 AC: 1218 AN: 10134

Middle Eastern (MID) AF: 0.0685 AC: 20 AN: 292

European-Non Finnish (NFE) AF: 0.124 AC: 8331 AN: 67292

Other (OTH) AF: 0.112 AC: 232 AN: 2066

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
PhyloP100		-0.068
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: rs1565560; hg19: chr15-40062825;