rs10510634

Variant names:

• chr3-30305477-A-G
• rs10510634
• XR_007095854.1:n.1269A>G

Variant summary

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

The XR_007095854.1(LOC124909358):​n.1269A>G 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 0.157 in 152,222 control chromosomes in the GnomAD database, including 1,919 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 0.16 (1919 hom., cov: 32)
• Consequence: LOC124909358 XR_007095854.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.80
• Publications: 16 publications found

Genes affected

LOC124909358 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23873 AN: 152104 Hom.: 1919 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.157 AC: 23871 AN: 152222 Hom.: 1919 Cov.: 32 AF XY: 0.153 AC XY: 11406 AN XY: 74426

African (AFR) AF: 0.121 AC: 5021 AN: 41542

American (AMR) AF: 0.139 AC: 2127 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 636 AN: 3470

East Asian (EAS) AF: 0.106 AC: 548 AN: 5174

South Asian (SAS) AF: 0.111 AC: 538 AN: 4826

European-Finnish (FIN) AF: 0.166 AC: 1758 AN: 10604

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12656 AN: 68006

Other (OTH) AF: 0.157 AC: 332 AN: 2114

Alfa AF: 0.167 Hom.: 2171

Bravo AF: 0.152

Asia WGS AF: 0.120 AC: 418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	13
DANN	Benign	0.74
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs10510634; hg19: chr3-30346968;