rs947465

Variant names:

• chr20-6147554-G-A
• rs947465

Your query was ambiguous. Multiple possible variants found:

• chr20-6147554-G-A
• chr20-6147554-G-T

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 0.104 in 152,228 control chromosomes in the GnomAD database, including 1,056 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 0.10 (1056 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.969
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.23 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: 0.104 AC: 15774 AN: 152110 Hom.: 1047 Cov.: 31

Gnomad AFR AF: 0.0367

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.0984

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.104 AC: 15800 AN: 152228 Hom.: 1056 Cov.: 31 AF XY: 0.107 AC XY: 7935 AN XY: 74438

African (AFR) AF: 0.0367 AC: 1525 AN: 41548

American (AMR) AF: 0.179 AC: 2735 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 386 AN: 3468

East Asian (EAS) AF: 0.241 AC: 1247 AN: 5170

South Asian (SAS) AF: 0.159 AC: 766 AN: 4820

European-Finnish (FIN) AF: 0.0984 AC: 1043 AN: 10598

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.114 AC: 7747 AN: 68006

Other (OTH) AF: 0.126 AC: 267 AN: 2116

Alfa AF: 0.113 Hom.: 858

Bravo AF: 0.108

Asia WGS AF: 0.223 AC: 775 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.8
DANN	Benign	0.74
PhyloP100		0.97

Splicing

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

Other links and lift over

dbSNP: rs947465; hg19: chr20-6128201;