chr20-22644378-A-T

Variant names:

• chr20-22644378-A-T
• rs6082762

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 0.705 in 151,962 control chromosomes in the GnomAD database, including 39,356 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 0.70 (39356 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.56
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.705 AC: 107056 AN: 151844 Hom.: 39344 Cov.: 31

Gnomad AFR AF: 0.479

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.806

Gnomad ASJ AF: 0.737

Gnomad EAS AF: 0.819

Gnomad SAS AF: 0.836

Gnomad FIN AF: 0.812

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.782

Gnomad OTH AF: 0.706

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

GnomAD4 genome AF: 0.705 AC: 107102 AN: 151962 Hom.: 39356 Cov.: 31 AF XY: 0.711 AC XY: 52792 AN XY: 74258

African (AFR) AF: 0.478 AC: 19804 AN: 41408

American (AMR) AF: 0.806 AC: 12328 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.737 AC: 2557 AN: 3470

East Asian (EAS) AF: 0.818 AC: 4197 AN: 5128

South Asian (SAS) AF: 0.837 AC: 4032 AN: 4818

European-Finnish (FIN) AF: 0.812 AC: 8584 AN: 10568

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.782 AC: 53181 AN: 67968

Other (OTH) AF: 0.709 AC: 1495 AN: 2110

Alfa AF: 0.728 Hom.: 5149

Bravo AF: 0.693

Asia WGS AF: 0.770 AC: 2678 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.25
DANN	Benign	0.60
PhyloP100		-3.6

Splicing

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

Other links and lift over

dbSNP: rs6082762; hg19: chr20-22625016;