rs834829

Variant names:

• chr2-156344337-A-G
• rs834829

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.556 in 152,146 control chromosomes in the GnomAD database, including 26,315 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 0.56 (26315 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.61

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.32).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.7 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: 0.556 AC: 84590 AN: 152026 Hom.: 26309 Cov.: 33

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.742

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.556 AC: 84604 AN: 152146 Hom.: 26315 Cov.: 33 AF XY: 0.558 AC XY: 41470 AN XY: 74378

Gnomad4 AFR AF: 0.271

Gnomad4 AMR AF: 0.511

Gnomad4 ASJ AF: 0.742

Gnomad4 EAS AF: 0.458

Gnomad4 SAS AF: 0.606

Gnomad4 FIN AF: 0.724

Gnomad4 NFE AF: 0.705

Gnomad4 OTH AF: 0.602

Alfa AF: 0.596 Hom.: 4614

Bravo AF: 0.519

Asia WGS AF: 0.558 AC: 1941 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
CADD	Benign	20
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs834829; hg19: chr2-157200849;