10-13234751-G-C

Variant names:

• chr10-13234751-G-C
• rs17152980

Variant summary

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

The variant allele was found at a frequency of 0.0997 in 152,168 control chromosomes in the GnomAD database, including 981 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 0.10 (981 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0998 AC: 15178 AN: 152050 Hom.: 981 Cov.: 30

Gnomad AFR AF: 0.0246

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.0705

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.0997 AC: 15170 AN: 152168 Hom.: 981 Cov.: 30 AF XY: 0.0995 AC XY: 7399 AN XY: 74388

African (AFR) AF: 0.0245 AC: 1019 AN: 41520

American (AMR) AF: 0.118 AC: 1805 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 654 AN: 3468

East Asian (EAS) AF: 0.227 AC: 1168 AN: 5150

South Asian (SAS) AF: 0.164 AC: 790 AN: 4822

European-Finnish (FIN) AF: 0.0705 AC: 748 AN: 10604

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8562 AN: 68004

Other (OTH) AF: 0.129 AC: 273 AN: 2112

Alfa AF: 0.0525 Hom.: 38

Bravo AF: 0.0989

Asia WGS AF: 0.181 AC: 630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.6
DANN	Benign	0.53
PhyloP100		-0.13
PromoterAI		0.017	Neutral

Splicing

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

Other links and lift over

dbSNP: rs17152980; hg19: chr10-13276751;