20-6782072-C-T

Variant names:

• chr20-6782072-C-T
• rs235772

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 0.673 in 151,978 control chromosomes in the GnomAD database, including 34,805 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 0.67 (34805 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.57
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.802 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: 0.673 AC: 102135 AN: 151860 Hom.: 34767 Cov.: 32

Gnomad AFR AF: 0.740

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.700

Gnomad ASJ AF: 0.822

Gnomad EAS AF: 0.823

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.697

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

GnomAD4 genome AF: 0.673 AC: 102229 AN: 151978 Hom.: 34805 Cov.: 32 AF XY: 0.670 AC XY: 49790 AN XY: 74278

African (AFR) AF: 0.740 AC: 30683 AN: 41472

American (AMR) AF: 0.700 AC: 10684 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.822 AC: 2854 AN: 3470

East Asian (EAS) AF: 0.822 AC: 4253 AN: 5172

South Asian (SAS) AF: 0.610 AC: 2932 AN: 4806

European-Finnish (FIN) AF: 0.578 AC: 6092 AN: 10546

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.625 AC: 42466 AN: 67938

Other (OTH) AF: 0.699 AC: 1473 AN: 2108

Alfa AF: 0.644 Hom.: 132526

Bravo AF: 0.687

Asia WGS AF: 0.724 AC: 2515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.036
DANN	Benign	0.19
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs235772; hg19: chr20-6762719;