20-46095666-A-G

Variant names:

• chr20-46095666-A-G
• rs6131010

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 0.785 in 152,242 control chromosomes in the GnomAD database, including 47,627 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 0.79 (47627 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0510

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.926 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: 0.785 AC: 119383 AN: 152124 Hom.: 47559 Cov.: 33

Gnomad AFR AF: 0.933

Gnomad AMI AF: 0.760

Gnomad AMR AF: 0.769

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.710

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.729

Gnomad OTH AF: 0.764

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

GnomAD4 genome AF: 0.785 AC: 119512 AN: 152242 Hom.: 47627 Cov.: 33 AF XY: 0.780 AC XY: 58069 AN XY: 74440

Gnomad4 AFR AF: 0.933

Gnomad4 AMR AF: 0.770

Gnomad4 ASJ AF: 0.705

Gnomad4 EAS AF: 0.622

Gnomad4 SAS AF: 0.756

Gnomad4 FIN AF: 0.710

Gnomad4 NFE AF: 0.729

Gnomad4 OTH AF: 0.766

Alfa AF: 0.786 Hom.: 8342

Bravo AF: 0.797

Asia WGS AF: 0.750 AC: 2610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.1
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: rs6131010; hg19: chr20-44724305;