15-39759553-C-T

Variant names:

• chr15-39759553-C-T
• rs10520151
• NM_152597.5:c.559+4268G>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.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 NM_152597.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0600
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
FSIP1	NM_152597.5	c.559+4268G>A		intron_variant	Intron 5 of 11	ENST00000350221.4	NP_689810.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FSIP1	ENST00000350221.4	c.559+4268G>A		intron_variant	Intron 5 of 11	1	NM_152597.5	ENSP00000280236.3

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

African (AFR) AF: 0.116 AC: 4806 AN: 41530

American (AMR) AF: 0.229 AC: 3498 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1051 AN: 3470

East Asian (EAS) AF: 0.0305 AC: 158 AN: 5182

South Asian (SAS) AF: 0.158 AC: 762 AN: 4822

European-Finnish (FIN) AF: 0.373 AC: 3940 AN: 10564

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.380 AC: 25830 AN: 67986

Other (OTH) AF: 0.263 AC: 557 AN: 2114

Alfa AF: 0.336 Hom.: 17488

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
PhyloP100		0.060
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: rs10520151; hg19: chr15-40051754;