15-39755505-T-A

Position:

• chr15-39755505-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152597.5(FSIP1):​c.559+8316A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,156 control chromosomes in the GnomAD database, including 953 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 0.10 (953 hom., cov: 32)
• Consequence: FSIP1 NM_152597.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.170

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FSIP1	NM_152597.5	c.559+8316A>T		intron_variant		ENST00000350221.4	NP_689810.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FSIP1	ENST00000350221.4	c.559+8316A>T		intron_variant		1	NM_152597.5	ENSP00000280236	P1

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15674 AN: 152038 Hom.: 955 Cov.: 32

Gnomad AFR AF: 0.0497

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.0961

Gnomad FIN AF: 0.0802

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.103 AC: 15673 AN: 152156 Hom.: 953 Cov.: 32 AF XY: 0.101 AC XY: 7544 AN XY: 74390

Gnomad4 AFR AF: 0.0496

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.209

Gnomad4 SAS AF: 0.0964

Gnomad4 FIN AF: 0.0802

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.135

Alfa AF: 0.0395 Hom.: 39

Bravo AF: 0.107

Asia WGS AF: 0.117 AC: 407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.7
DANN	Benign	0.79

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: rs12911842; hg19: chr15-40047706;