20-3667731-A-G

Position:

• chr20-3667731-A-G

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 0.73 in 152,118 control chromosomes in the GnomAD database, including 40,999 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 0.73 (40999 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.994

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.730 AC: 110943 AN: 151998 Hom.: 40973 Cov.: 32

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.755

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.715

Gnomad FIN AF: 0.562

Gnomad MID AF: 0.729

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.743

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

GnomAD4 genome AF: 0.730 AC: 111027 AN: 152118 Hom.: 40999 Cov.: 32 AF XY: 0.724 AC XY: 53812 AN XY: 74356

Gnomad4 AFR AF: 0.837

Gnomad4 AMR AF: 0.755

Gnomad4 ASJ AF: 0.733

Gnomad4 EAS AF: 0.629

Gnomad4 SAS AF: 0.714

Gnomad4 FIN AF: 0.562

Gnomad4 NFE AF: 0.695

Gnomad4 OTH AF: 0.743

Alfa AF: 0.709 Hom.: 50771

Bravo AF: 0.749

Asia WGS AF: 0.714 AC: 2486 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	6.7
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs512625; hg19: chr20-3648378;