20-40130189-G-A

Variant names:

• chr20-40130189-G-A
• rs735998

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 0.447 in 151,976 control chromosomes in the GnomAD database, including 16,825 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 0.45 (16825 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.239
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67951 AN: 151858 Hom.: 16817 Cov.: 33

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.634

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.447 AC: 67987 AN: 151976 Hom.: 16825 Cov.: 33 AF XY: 0.449 AC XY: 33348 AN XY: 74302

African (AFR) AF: 0.231 AC: 9576 AN: 41434

American (AMR) AF: 0.490 AC: 7477 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.496 AC: 1719 AN: 3468

East Asian (EAS) AF: 0.634 AC: 3271 AN: 5158

South Asian (SAS) AF: 0.544 AC: 2624 AN: 4824

European-Finnish (FIN) AF: 0.472 AC: 4974 AN: 10546

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.540 AC: 36699 AN: 67970

Other (OTH) AF: 0.471 AC: 991 AN: 2106

Alfa AF: 0.495 Hom.: 7025

Bravo AF: 0.440

Asia WGS AF: 0.525 AC: 1825 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.2
DANN	Benign	0.31
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs735998; hg19: chr20-38758830;