15-39746955-C-T

Position:

• chr15-39746955-C-T

Variant summary

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

The ENST00000350221.4(FSIP1):​c.560-5055G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 151,850 control chromosomes in the GnomAD database, including 14,353 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 0.43 (14353 hom., cov: 30)
• Consequence: FSIP1 ENST00000350221.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.318

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FSIP1	NM_152597.5	c.560-5055G>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.560-5055G>A		intron_variant		1	NM_152597.5	ENSP00000280236	P1
FSIP1	ENST00000559692.1	n.146+347G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64763 AN: 151732 Hom.: 14339 Cov.: 30

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.427 AC: 64817 AN: 151850 Hom.: 14353 Cov.: 30 AF XY: 0.432 AC XY: 32057 AN XY: 74196

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.528

Gnomad4 ASJ AF: 0.371

Gnomad4 EAS AF: 0.477

Gnomad4 SAS AF: 0.344

Gnomad4 FIN AF: 0.563

Gnomad4 NFE AF: 0.446

Gnomad4 OTH AF: 0.411

Alfa AF: 0.431 Hom.: 2868

Bravo AF: 0.426

Asia WGS AF: 0.428 AC: 1490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.18

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: rs4115216; hg19: chr15-40039156;