rs985162

Positions:

• chr2-129409778-T-C

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 0.456 in 151,792 control chromosomes in the GnomAD database, including 17,676 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 0.46 (17676 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0780

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.676 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: 0.456 AC: 69126 AN: 151676 Hom.: 17644 Cov.: 32

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.668

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.456 AC: 69212 AN: 151792 Hom.: 17676 Cov.: 32 AF XY: 0.456 AC XY: 33830 AN XY: 74210

Gnomad4 AFR AF: 0.682

Gnomad4 AMR AF: 0.471

Gnomad4 ASJ AF: 0.377

Gnomad4 EAS AF: 0.669

Gnomad4 SAS AF: 0.373

Gnomad4 FIN AF: 0.364

Gnomad4 NFE AF: 0.324

Gnomad4 OTH AF: 0.458

Alfa AF: 0.354 Hom.: 16477

Bravo AF: 0.475

Asia WGS AF: 0.555 AC: 1916 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.4
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: rs985162; hg19: chr2-130167351;