rs180643

Variant names:

• chr10-116008666-A-G
• rs180643

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 0.619 in 152,070 control chromosomes in the GnomAD database, including 31,639 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 0.62 (31639 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.479
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.748 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: 0.619 AC: 94117 AN: 151952 Hom.: 31634 Cov.: 33

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.833

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.783

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.755

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.754

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.619 AC: 94144 AN: 152070 Hom.: 31639 Cov.: 33 AF XY: 0.620 AC XY: 46100 AN XY: 74356

African (AFR) AF: 0.349 AC: 14455 AN: 41438

American (AMR) AF: 0.665 AC: 10158 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.783 AC: 2716 AN: 3470

East Asian (EAS) AF: 0.427 AC: 2202 AN: 5158

South Asian (SAS) AF: 0.643 AC: 3101 AN: 4822

European-Finnish (FIN) AF: 0.755 AC: 7999 AN: 10588

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.754 AC: 51266 AN: 68000

Other (OTH) AF: 0.618 AC: 1307 AN: 2116

Alfa AF: 0.665 Hom.: 4621

Bravo AF: 0.601

Asia WGS AF: 0.546 AC: 1897 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.2
DANN	Benign	0.70
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs180643; hg19: chr10-117768177;