15-39746232-T-C

Position:

• chr15-39746232-T-C

Variant summary

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

The NM_152597.5(FSIP1):​c.560-4332A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 151,836 control chromosomes in the GnomAD database, including 4,086 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 0.20 (4086 hom., cov: 32)
• Consequence: FSIP1 NM_152597.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.516

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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FSIP1	NM_152597.5	c.560-4332A>G		intron_variant		ENST00000350221.4	NP_689810.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FSIP1	ENST00000350221.4	c.560-4332A>G		intron_variant		1	NM_152597.5	ENSP00000280236	P1
FSIP1	ENST00000559692.1	n.146+1070A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30089 AN: 151718 Hom.: 4078 Cov.: 32

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.0747

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0914

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.198 AC: 30134 AN: 151836 Hom.: 4086 Cov.: 32 AF XY: 0.205 AC XY: 15241 AN XY: 74242

Gnomad4 AFR AF: 0.309

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.450

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.196

Gnomad4 NFE AF: 0.0914

Gnomad4 OTH AF: 0.187

Alfa AF: 0.124 Hom.: 4089

Bravo AF: 0.217

Asia WGS AF: 0.341 AC: 1187 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.45

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: rs8033957; hg19: chr15-40038433;