rs10498071

Positions:

• chr2-219857977-G-A

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 0.0922 in 152,238 control chromosomes in the GnomAD database, including 695 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 0.092 (695 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0300

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0922 AC: 14023 AN: 152120 Hom.: 692 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.0737

Gnomad ASJ AF: 0.0986

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.0608

Gnomad FIN AF: 0.0521

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0885

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.0922 AC: 14035 AN: 152238 Hom.: 695 Cov.: 32 AF XY: 0.0894 AC XY: 6657 AN XY: 74438

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.0736

Gnomad4 ASJ AF: 0.0986

Gnomad4 EAS AF: 0.133

Gnomad4 SAS AF: 0.0602

Gnomad4 FIN AF: 0.0521

Gnomad4 NFE AF: 0.0885

Gnomad4 OTH AF: 0.101

Alfa AF: 0.0888 Hom.: 868

Bravo AF: 0.0946

Asia WGS AF: 0.114 AC: 397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.4
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10498071; hg19: chr2-220722698;