chr20-46310212-T-C

Variant names:

• chr20-46310212-T-C
• rs6032769

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 0.741 in 152,212 control chromosomes in the GnomAD database, including 41,855 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 0.74 (41855 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.74 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: 0.741 AC: 112660 AN: 152094 Hom.: 41824 Cov.: 34

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.746

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.734

Gnomad FIN AF: 0.742

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.737

Gnomad OTH AF: 0.777

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

GnomAD4 genome AF: 0.741 AC: 112743 AN: 152212 Hom.: 41855 Cov.: 34 AF XY: 0.740 AC XY: 55090 AN XY: 74428

African (AFR) AF: 0.747 AC: 31021 AN: 41514

American (AMR) AF: 0.746 AC: 11411 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.810 AC: 2813 AN: 3472

East Asian (EAS) AF: 0.640 AC: 3316 AN: 5180

South Asian (SAS) AF: 0.735 AC: 3542 AN: 4822

European-Finnish (FIN) AF: 0.742 AC: 7862 AN: 10598

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.737 AC: 50134 AN: 68002

Other (OTH) AF: 0.775 AC: 1639 AN: 2116

Alfa AF: 0.743 Hom.: 162312

Bravo AF: 0.744

Asia WGS AF: 0.691 AC: 2403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	7.1
DANN	Benign	0.77
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs6032769; hg19: chr20-44938851;