rs834829

Positions:

• chr2-156344337-A-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;