2-163205924-C-T

Position:

• chr2-163205924-C-T

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 0.898 in 151,980 control chromosomes in the GnomAD database, including 61,523 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 0.90 (61523 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.658

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.936 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: 0.898 AC: 136420 AN: 151862 Hom.: 61511 Cov.: 30

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.909

Gnomad AMR AF: 0.910

Gnomad ASJ AF: 0.938

Gnomad EAS AF: 0.903

Gnomad SAS AF: 0.868

Gnomad FIN AF: 0.932

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.942

Gnomad OTH AF: 0.896

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

GnomAD4 genome AF: 0.898 AC: 136478 AN: 151980 Hom.: 61523 Cov.: 30 AF XY: 0.895 AC XY: 66506 AN XY: 74268

Gnomad4 AFR AF: 0.811

Gnomad4 AMR AF: 0.910

Gnomad4 ASJ AF: 0.938

Gnomad4 EAS AF: 0.904

Gnomad4 SAS AF: 0.868

Gnomad4 FIN AF: 0.932

Gnomad4 NFE AF: 0.942

Gnomad4 OTH AF: 0.894

Alfa AF: 0.919 Hom.: 8006

Bravo AF: 0.892

Asia WGS AF: 0.878 AC: 3055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	3.3
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2036524; hg19: chr2-164062434;