2-163581265-T-C

Variant names:

• chr2-163581265-T-C
• rs2083482

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 0.461 in 151,754 control chromosomes in the GnomAD database, including 16,507 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 (16507 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.391
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.52 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: 0.460 AC: 69827 AN: 151636 Hom.: 16493 Cov.: 30

Gnomad AFR AF: 0.404

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.461 AC: 69883 AN: 151754 Hom.: 16507 Cov.: 30 AF XY: 0.455 AC XY: 33760 AN XY: 74128

African (AFR) AF: 0.404 AC: 16722 AN: 41390

American (AMR) AF: 0.414 AC: 6319 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1313 AN: 3462

East Asian (EAS) AF: 0.198 AC: 1019 AN: 5150

South Asian (SAS) AF: 0.459 AC: 2200 AN: 4796

European-Finnish (FIN) AF: 0.505 AC: 5297 AN: 10492

Middle Eastern (MID) AF: 0.370 AC: 108 AN: 292

European-Non Finnish (NFE) AF: 0.524 AC: 35605 AN: 67892

Other (OTH) AF: 0.437 AC: 921 AN: 2106

Alfa AF: 0.485 Hom.: 10617

Bravo AF: 0.444

Asia WGS AF: 0.372 AC: 1296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.41
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs2083482; hg19: chr2-164437775;