2-10439098-G-C

Variant names:

• chr2-10439098-G-C
• rs818162

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 0.733 in 152,184 control chromosomes in the GnomAD database, including 41,325 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 0.73 (41325 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.390

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.811 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: 0.733 AC: 111435 AN: 152066 Hom.: 41305 Cov.: 33

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.831

Gnomad SAS AF: 0.803

Gnomad FIN AF: 0.807

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.680

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

GnomAD4 genome AF: 0.733 AC: 111504 AN: 152184 Hom.: 41325 Cov.: 33 AF XY: 0.739 AC XY: 54974 AN XY: 74424

Gnomad4 AFR AF: 0.794

Gnomad4 AMR AF: 0.665

Gnomad4 ASJ AF: 0.605

Gnomad4 EAS AF: 0.832

Gnomad4 SAS AF: 0.801

Gnomad4 FIN AF: 0.807

Gnomad4 NFE AF: 0.695

Gnomad4 OTH AF: 0.684

Alfa AF: 0.718 Hom.: 4865

Bravo AF: 0.725

Asia WGS AF: 0.809 AC: 2816 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.37
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs818162; hg19: chr2-10579224;