20-47947062-A-T

Variant names:

• chr20-47947062-A-T
• rs10211734

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 0.0979 in 152,212 control chromosomes in the GnomAD database, including 1,102 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 0.098 (1102 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330
• Publications: 1 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 = 0.408 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: 0.0977 AC: 14865 AN: 152094 Hom.: 1099 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0675

Gnomad ASJ AF: 0.0446

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.0922

Gnomad FIN AF: 0.0569

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0712

Gnomad OTH AF: 0.0912

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

GnomAD4 genome AF: 0.0979 AC: 14894 AN: 152212 Hom.: 1102 Cov.: 32 AF XY: 0.0994 AC XY: 7395 AN XY: 74428

African (AFR) AF: 0.129 AC: 5372 AN: 41510

American (AMR) AF: 0.0673 AC: 1029 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0446 AC: 155 AN: 3472

East Asian (EAS) AF: 0.423 AC: 2185 AN: 5164

South Asian (SAS) AF: 0.0916 AC: 442 AN: 4824

European-Finnish (FIN) AF: 0.0569 AC: 604 AN: 10608

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0712 AC: 4843 AN: 68020

Other (OTH) AF: 0.0964 AC: 204 AN: 2116

Alfa AF: 0.0827 Hom.: 80

Bravo AF: 0.103

Asia WGS AF: 0.247 AC: 857 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.3
DANN	Benign	0.65
PhyloP100		-0.033

Splicing

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

Other links and lift over

dbSNP: rs10211734; hg19: chr20-46575806;