20-4371457-A-G

Variant names:

• chr20-4371457-A-G
• rs159788

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 0.851 in 152,192 control chromosomes in the GnomAD database, including 55,272 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 0.85 (55272 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.37
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.89 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: 0.851 AC: 129438 AN: 152074 Hom.: 55228 Cov.: 31

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.914

Gnomad AMR AF: 0.903

Gnomad ASJ AF: 0.867

Gnomad EAS AF: 0.720

Gnomad SAS AF: 0.785

Gnomad FIN AF: 0.814

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.880

Gnomad OTH AF: 0.871

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

GnomAD4 genome AF: 0.851 AC: 129530 AN: 152192 Hom.: 55272 Cov.: 31 AF XY: 0.847 AC XY: 63032 AN XY: 74410

African (AFR) AF: 0.815 AC: 33836 AN: 41508

American (AMR) AF: 0.903 AC: 13811 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.867 AC: 3009 AN: 3472

East Asian (EAS) AF: 0.720 AC: 3717 AN: 5160

South Asian (SAS) AF: 0.786 AC: 3795 AN: 4830

European-Finnish (FIN) AF: 0.814 AC: 8630 AN: 10596

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.880 AC: 59820 AN: 68008

Other (OTH) AF: 0.862 AC: 1820 AN: 2112

Alfa AF: 0.870 Hom.: 119935

Bravo AF: 0.856

Asia WGS AF: 0.732 AC: 2548 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.41
DANN	Benign	0.37
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs159788; hg19: chr20-4352104;