15-39759553-C-T

Position:

• chr15-39759553-C-T

Variant summary

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

The ENST00000350221.4(FSIP1):​c.559+4268G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 152,148 control chromosomes in the GnomAD database, including 6,717 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 0.27 (6717 hom., cov: 32)
• Consequence: FSIP1 ENST00000350221.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0600

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 (NFE) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FSIP1	NM_152597.5	c.559+4268G>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.559+4268G>A		intron_variant		1	NM_152597.5	ENSP00000280236	P1

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40961 AN: 152030 Hom.: 6715 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.0306

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.269 AC: 40977 AN: 152148 Hom.: 6717 Cov.: 32 AF XY: 0.266 AC XY: 19779 AN XY: 74344

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.229

Gnomad4 ASJ AF: 0.303

Gnomad4 EAS AF: 0.0305

Gnomad4 SAS AF: 0.158

Gnomad4 FIN AF: 0.373

Gnomad4 NFE AF: 0.380

Gnomad4 OTH AF: 0.263

Alfa AF: 0.349 Hom.: 13384

Bravo AF: 0.253

Asia WGS AF: 0.101 AC: 352 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	1.3
DANN	Benign	0.63

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: rs10520151; hg19: chr15-40051754;