20-238370-A-G

Variant names:

• chr20-238370-A-G
• rs1418259

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 0.616 in 152,072 control chromosomes in the GnomAD database, including 30,092 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 0.62 (30092 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.576
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.804 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: 0.616 AC: 93668 AN: 151954 Hom.: 30063 Cov.: 32

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.616 AC: 93743 AN: 152072 Hom.: 30092 Cov.: 32 AF XY: 0.615 AC XY: 45683 AN XY: 74322

African (AFR) AF: 0.811 AC: 33672 AN: 41498

American (AMR) AF: 0.537 AC: 8204 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.582 AC: 2015 AN: 3464

East Asian (EAS) AF: 0.545 AC: 2814 AN: 5168

South Asian (SAS) AF: 0.650 AC: 3134 AN: 4824

European-Finnish (FIN) AF: 0.532 AC: 5619 AN: 10554

Middle Eastern (MID) AF: 0.541 AC: 158 AN: 292

European-Non Finnish (NFE) AF: 0.538 AC: 36568 AN: 67970

Other (OTH) AF: 0.551 AC: 1164 AN: 2114

Alfa AF: 0.578 Hom.: 14971

Bravo AF: 0.621

Asia WGS AF: 0.564 AC: 1966 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	3.0
DANN	Benign	0.66
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs1418259; hg19: chr20-219011;