20-7642179-A-G

Variant names:

• chr20-7642179-A-G
• rs6086141

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 0.446 in 149,112 control chromosomes in the GnomAD database, including 15,482 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 (15482 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.278
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.85 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: 0.446 AC: 66493 AN: 149034 Hom.: 15463 Cov.: 30

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.872

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.446 AC: 66544 AN: 149112 Hom.: 15482 Cov.: 30 AF XY: 0.449 AC XY: 32588 AN XY: 72570

African (AFR) AF: 0.379 AC: 15365 AN: 40586

American (AMR) AF: 0.530 AC: 7977 AN: 15044

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1561 AN: 3460

East Asian (EAS) AF: 0.871 AC: 4467 AN: 5128

South Asian (SAS) AF: 0.624 AC: 2975 AN: 4768

European-Finnish (FIN) AF: 0.357 AC: 3324 AN: 9312

Middle Eastern (MID) AF: 0.503 AC: 146 AN: 290

European-Non Finnish (NFE) AF: 0.434 AC: 29305 AN: 67552

Other (OTH) AF: 0.488 AC: 1013 AN: 2074

Alfa AF: 0.416 Hom.: 1678

Bravo AF: 0.457

Asia WGS AF: 0.743 AC: 2583 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.2
DANN	Benign	0.61
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs6086141; hg19: chr20-7622826;