20-6423634-C-A

Variant names:

• chr20-6423634-C-A
• rs961253

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 0.332 in 151,762 control chromosomes in the GnomAD database, including 8,643 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 0.33 (8643 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.759
• Publications: 164 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50406 AN: 151646 Hom.: 8642 Cov.: 32

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.0942

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.332 AC: 50430 AN: 151762 Hom.: 8643 Cov.: 32 AF XY: 0.330 AC XY: 24448 AN XY: 74142

African (AFR) AF: 0.349 AC: 14454 AN: 41358

American (AMR) AF: 0.306 AC: 4665 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 1131 AN: 3464

East Asian (EAS) AF: 0.0944 AC: 488 AN: 5168

South Asian (SAS) AF: 0.308 AC: 1486 AN: 4818

European-Finnish (FIN) AF: 0.290 AC: 3046 AN: 10492

Middle Eastern (MID) AF: 0.342 AC: 100 AN: 292

European-Non Finnish (NFE) AF: 0.353 AC: 23964 AN: 67904

Other (OTH) AF: 0.331 AC: 697 AN: 2108

Alfa AF: 0.341 Hom.: 36675

Bravo AF: 0.331

Asia WGS AF: 0.246 AC: 856 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.8
DANN	Benign	0.45
PhyloP100		0.76

Splicing

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

Other links and lift over

dbSNP: rs961253; hg19: chr20-6404281;