chr13-53393956-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

Genes affected

ENSG00000273919 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.164 AC: 6819 AN: 41488

American (AMR) AF: 0.0766 AC: 1169 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0736 AC: 255 AN: 3464

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5170

South Asian (SAS) AF: 0.0824 AC: 398 AN: 4828

European-Finnish (FIN) AF: 0.0859 AC: 910 AN: 10590

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7870 AN: 67990

Other (OTH) AF: 0.105 AC: 223 AN: 2114

Alfa AF: 0.115 Hom.: 2919

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
PhyloP100		0.030

Splicing

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

Other links and lift over

dbSNP: rs10507577; hg19: chr13-53968091;