20-22644378-A-T

Variant names:

• chr20-22644378-A-T
• rs6082762

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.478

Gnomad4 AMR AF: 0.806

Gnomad4 ASJ AF: 0.737

Gnomad4 EAS AF: 0.818

Gnomad4 SAS AF: 0.837

Gnomad4 FIN AF: 0.812

Gnomad4 NFE AF: 0.782

Gnomad4 OTH AF: 0.709

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6082762; hg19: chr20-22625016;