20-40358946-G-A

Variant names:

• chr20-40358946-G-A
• rs728331

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 0.144 in 152,094 control chromosomes in the GnomAD database, including 2,451 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 0.14 (2451 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.312 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: 0.144 AC: 21899 AN: 151976 Hom.: 2439 Cov.: 32

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0903

Gnomad ASJ AF: 0.0814

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0622

Gnomad FIN AF: 0.0417

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0889

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.144 AC: 21945 AN: 152094 Hom.: 2451 Cov.: 32 AF XY: 0.140 AC XY: 10433 AN XY: 74358

African (AFR) AF: 0.316 AC: 13104 AN: 41430

American (AMR) AF: 0.0900 AC: 1376 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0814 AC: 282 AN: 3466

East Asian (EAS) AF: 0.00155 AC: 8 AN: 5174

South Asian (SAS) AF: 0.0629 AC: 303 AN: 4818

European-Finnish (FIN) AF: 0.0417 AC: 442 AN: 10596

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0889 AC: 6047 AN: 68010

Other (OTH) AF: 0.129 AC: 273 AN: 2110

Alfa AF: 0.0708 Hom.: 136

Bravo AF: 0.155

Asia WGS AF: 0.0610 AC: 211 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.20
PhyloP100		0.043

Splicing

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

Other links and lift over

dbSNP: rs728331; hg19: chr20-38987586;