2-61649830-T-C

Variant names:

• chr2-61649830-T-C
• rs2421332

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 0.271 in 152,004 control chromosomes in the GnomAD database, including 6,308 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 0.27 (6308 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.196
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.271 AC: 41148 AN: 151884 Hom.: 6299 Cov.: 31

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.0856

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.271 AC: 41175 AN: 152004 Hom.: 6308 Cov.: 31 AF XY: 0.266 AC XY: 19800 AN XY: 74324

African (AFR) AF: 0.398 AC: 16465 AN: 41410

American (AMR) AF: 0.198 AC: 3031 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1092 AN: 3472

East Asian (EAS) AF: 0.0858 AC: 443 AN: 5164

South Asian (SAS) AF: 0.155 AC: 749 AN: 4824

European-Finnish (FIN) AF: 0.179 AC: 1890 AN: 10584

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16427 AN: 67966

Other (OTH) AF: 0.268 AC: 566 AN: 2110

Alfa AF: 0.255 Hom.: 8841

Bravo AF: 0.279

Asia WGS AF: 0.133 AC: 463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	7.1
DANN	Benign	0.77
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs2421332; hg19: chr2-61876965;