rs10496604

Variant names:

• chr2-123028181-G-A
• rs10496604

Your query was ambiguous. Multiple possible variants found:

• chr2-123028181-G-A
• chr2-123028181-G-C

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 0.667 in 151,926 control chromosomes in the GnomAD database, including 34,760 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 0.67 (34760 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.560
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.807 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: 0.667 AC: 101235 AN: 151810 Hom.: 34702 Cov.: 31

Gnomad AFR AF: 0.814

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.728

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.697

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.668

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

GnomAD4 genome AF: 0.667 AC: 101353 AN: 151926 Hom.: 34760 Cov.: 31 AF XY: 0.663 AC XY: 49239 AN XY: 74226

African (AFR) AF: 0.814 AC: 33743 AN: 41458

American (AMR) AF: 0.728 AC: 11117 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.645 AC: 2237 AN: 3470

East Asian (EAS) AF: 0.697 AC: 3582 AN: 5140

South Asian (SAS) AF: 0.544 AC: 2622 AN: 4820

European-Finnish (FIN) AF: 0.509 AC: 5367 AN: 10542

Middle Eastern (MID) AF: 0.661 AC: 193 AN: 292

European-Non Finnish (NFE) AF: 0.596 AC: 40453 AN: 67916

Other (OTH) AF: 0.671 AC: 1413 AN: 2106

Alfa AF: 0.515 Hom.: 1462

Bravo AF: 0.694

Asia WGS AF: 0.664 AC: 2310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.21
DANN	Benign	0.61
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs10496604; hg19: chr2-123785757;