rs167391

Variant names:

• chr20-3098355-A-T
• rs167391

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 0.433 in 151,970 control chromosomes in the GnomAD database, including 14,720 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 0.43 (14720 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.975
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.52 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: 0.433 AC: 65722 AN: 151852 Hom.: 14699 Cov.: 32

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.433 AC: 65784 AN: 151970 Hom.: 14720 Cov.: 32 AF XY: 0.434 AC XY: 32214 AN XY: 74292

African (AFR) AF: 0.526 AC: 21803 AN: 41424

American (AMR) AF: 0.349 AC: 5327 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 1291 AN: 3472

East Asian (EAS) AF: 0.492 AC: 2550 AN: 5178

South Asian (SAS) AF: 0.428 AC: 2067 AN: 4826

European-Finnish (FIN) AF: 0.426 AC: 4496 AN: 10558

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.397 AC: 27007 AN: 67950

Other (OTH) AF: 0.410 AC: 865 AN: 2112

Alfa AF: 0.422 Hom.: 1716

Bravo AF: 0.426

Asia WGS AF: 0.458 AC: 1589 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.87
DANN	Benign	0.46
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs167391; hg19: chr20-3079001;