chr20-6640246-G-A

Variant names:

• chr20-6640246-G-A
• rs967417

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 0.416 in 151,822 control chromosomes in the GnomAD database, including 14,783 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 0.42 (14783 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.36
• Publications: 44 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.808 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: 0.416 AC: 63101 AN: 151702 Hom.: 14764 Cov.: 31

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.829

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.416 AC: 63147 AN: 151822 Hom.: 14783 Cov.: 31 AF XY: 0.426 AC XY: 31618 AN XY: 74196

African (AFR) AF: 0.214 AC: 8869 AN: 41398

American (AMR) AF: 0.529 AC: 8067 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1374 AN: 3468

East Asian (EAS) AF: 0.828 AC: 4261 AN: 5144

South Asian (SAS) AF: 0.367 AC: 1765 AN: 4812

European-Finnish (FIN) AF: 0.575 AC: 6064 AN: 10538

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.461 AC: 31308 AN: 67892

Other (OTH) AF: 0.419 AC: 884 AN: 2108

Alfa AF: 0.456 Hom.: 75878

Bravo AF: 0.407

Asia WGS AF: 0.553 AC: 1924 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.28
DANN	Benign	0.70
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs967417; hg19: chr20-6620893;