20-7466544-A-G

Variant names:

• chr20-7466544-A-G
• rs2326931

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 0.609 in 151,842 control chromosomes in the GnomAD database, including 28,367 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 0.61 (28367 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.726 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: 0.609 AC: 92347 AN: 151724 Hom.: 28347 Cov.: 32

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.746

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.609 AC: 92410 AN: 151842 Hom.: 28367 Cov.: 32 AF XY: 0.605 AC XY: 44888 AN XY: 74216

Gnomad4 AFR AF: 0.566

Gnomad4 AMR AF: 0.579

Gnomad4 ASJ AF: 0.638

Gnomad4 EAS AF: 0.745

Gnomad4 SAS AF: 0.540

Gnomad4 FIN AF: 0.592

Gnomad4 NFE AF: 0.638

Gnomad4 OTH AF: 0.610

Alfa AF: 0.622 Hom.: 3722

Bravo AF: 0.607

Asia WGS AF: 0.633 AC: 2197 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.6
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2326931; hg19: chr20-7447191;