10-31749565-C-T

Variant names:

• chr10-31749565-C-T
• rs10826987
• ENST00000815629.1:n.513G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000815629.1(ENSG00000306144):​n.513G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 152,140 control chromosomes in the GnomAD database, including 3,529 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 0.21 (3529 hom., cov: 33)
• Consequence: ENSG00000306144 ENST00000815629.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.190
• Publications: 1 publications found

Genes affected

ENSG00000306144 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000815629.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306144	ENST00000815629.1		n.513G>A		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000306144	ENST00000815630.1		n.266G>A		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31874 AN: 152020 Hom.: 3522 Cov.: 33

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.0969

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.210 AC: 31921 AN: 152140 Hom.: 3529 Cov.: 33 AF XY: 0.211 AC XY: 15665 AN XY: 74372

African (AFR) AF: 0.288 AC: 11940 AN: 41490

American (AMR) AF: 0.173 AC: 2639 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 857 AN: 3472

East Asian (EAS) AF: 0.228 AC: 1179 AN: 5166

South Asian (SAS) AF: 0.220 AC: 1064 AN: 4828

European-Finnish (FIN) AF: 0.177 AC: 1877 AN: 10588

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11738 AN: 67996

Other (OTH) AF: 0.226 AC: 474 AN: 2102

Alfa AF: 0.187 Hom.: 1439

Bravo AF: 0.216

Asia WGS AF: 0.244 AC: 846 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.17
DANN	Benign	0.70
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs10826987; hg19: chr10-32038493;