rs947465

chr20-6147554-G-Achr20-6147554-G-T

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 0.104 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0367

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.111

Gnomad4 EAS AF: 0.241

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.0984

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.126

Alfa AF: 0.113 Hom.: 613

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs947465; hg19: chr20-6128201;