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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.680

Gnomad4 AMR AF: 0.352

Gnomad4 ASJ AF: 0.223

Gnomad4 EAS AF: 0.471

Gnomad4 SAS AF: 0.279

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.353

Alfa AF: 0.255 Hom.: 11092

Bravo AF: 0.405

Asia WGS AF: 0.400 AC: 1392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10498070; hg19: chr2-220698125;