rs10507577

Variant names:

• chr13-53393956-T-C
• rs10507577
• ENST00000615176.1:n.976+3303T>C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000615176.1(ENSG00000273919):​n.976+3303T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,110 control chromosomes in the GnomAD database, including 1,113 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 0.12 (1113 hom., cov: 31)
• Consequence: ENSG00000273919 ENST00000615176.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0300

Genes affected

ENSG00000273919 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.22).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000273919	ENST00000615176.1	n.976+3303T>C		intron_variant	Intron 2 of 2	2
ENSG00000287722	ENST00000657016.1	n.629+89834T>C		intron_variant	Intron 2 of 3
ENSG00000288768	ENST00000688155.1	n.46-28824T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17800 AN: 151992 Hom.: 1112 Cov.: 31

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.0767

Gnomad ASJ AF: 0.0736

Gnomad EAS AF: 0.00174

Gnomad SAS AF: 0.0817

Gnomad FIN AF: 0.0859

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.117 AC: 17816 AN: 152110 Hom.: 1113 Cov.: 31 AF XY: 0.114 AC XY: 8478 AN XY: 74378

Gnomad4 AFR AF: 0.164

Gnomad4 AMR AF: 0.0766

Gnomad4 ASJ AF: 0.0736

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.0824

Gnomad4 FIN AF: 0.0859

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.105

Alfa AF: 0.111 Hom.: 1742

Bravo AF: 0.121

Asia WGS AF: 0.0490 AC: 171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.22
CADD	Benign	15
DANN	Benign	0.77

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10507577; hg19: chr13-53968091;