rs10507577

Positions:

• chr13-53393956-T-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, non coding transcript 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: ENST00000615176.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0300

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000615176.1	n.976+3303T>C		intron_variant, non_coding_transcript_variant		2
	ENST00000657016.1	n.629+89834T>C		intron_variant, non_coding_transcript_variant
	ENST00000688155.1	n.46-28824T>C		intron_variant, non_coding_transcript_variant

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;