2-162105535-T-C

Variant names:

• chr2-162105535-T-C
• rs2052401

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.462 in 152,078 control chromosomes in the GnomAD database, including 16,638 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 (16638 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.462 AC: 70132 AN: 151960 Hom.: 16606 Cov.: 32

Gnomad AFR AF: 0.536

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.681

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.462 AC: 70215 AN: 152078 Hom.: 16638 Cov.: 32 AF XY: 0.467 AC XY: 34731 AN XY: 74342

African (AFR) AF: 0.537 AC: 22252 AN: 41476

American (AMR) AF: 0.402 AC: 6141 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 1690 AN: 3470

East Asian (EAS) AF: 0.682 AC: 3524 AN: 5168

South Asian (SAS) AF: 0.515 AC: 2483 AN: 4822

European-Finnish (FIN) AF: 0.456 AC: 4812 AN: 10562

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.409 AC: 27821 AN: 67978

Other (OTH) AF: 0.443 AC: 936 AN: 2112

Alfa AF: 0.402 Hom.: 7166

Bravo AF: 0.463

Asia WGS AF: 0.552 AC: 1919 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.68
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs2052401; hg19: chr2-162962045;