rs10498070

Variant names:

• chr2-219833404-A-C
• rs10498070

Your query was ambiguous. Multiple possible variants found:

• chr2-219833404-A-C
• chr2-219833404-A-G
• chr2-219833404-A-T

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 0.381 in 152,102 control chromosomes in the GnomAD database, including 13,883 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 0.38 (13883 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.673 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: 0.381 AC: 57922 AN: 151984 Hom.: 13854 Cov.: 32

Gnomad AFR AF: 0.680

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.381 AC: 58006 AN: 152102 Hom.: 13883 Cov.: 32 AF XY: 0.381 AC XY: 28335 AN XY: 74346

African (AFR) AF: 0.680 AC: 28202 AN: 41468

American (AMR) AF: 0.352 AC: 5377 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 774 AN: 3470

East Asian (EAS) AF: 0.471 AC: 2436 AN: 5172

South Asian (SAS) AF: 0.279 AC: 1342 AN: 4810

European-Finnish (FIN) AF: 0.257 AC: 2729 AN: 10600

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.237 AC: 16119 AN: 67986

Other (OTH) AF: 0.353 AC: 744 AN: 2110

Alfa AF: 0.278 Hom.: 29879

Bravo AF: 0.405

Asia WGS AF: 0.400 AC: 1392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.9
DANN	Benign	0.50
PhyloP100		-0.070

Splicing

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

Other links and lift over

dbSNP: rs10498070; hg19: chr2-220698125;