20-6998506-G-A

Variant names:

• chr20-6998506-G-A
• rs6107905

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 0.648 in 152,110 control chromosomes in the GnomAD database, including 36,817 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 0.65 (36817 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.495
• 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 = 0.841 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.649 AC: 98611 AN: 151994 Hom.: 36815 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.749

Gnomad AMR AF: 0.773

Gnomad ASJ AF: 0.789

Gnomad EAS AF: 0.861

Gnomad SAS AF: 0.740

Gnomad FIN AF: 0.850

Gnomad MID AF: 0.758

Gnomad NFE AF: 0.804

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.648 AC: 98626 AN: 152110 Hom.: 36817 Cov.: 32 AF XY: 0.655 AC XY: 48706 AN XY: 74360

African (AFR) AF: 0.241 AC: 9985 AN: 41456

American (AMR) AF: 0.774 AC: 11833 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.789 AC: 2741 AN: 3472

East Asian (EAS) AF: 0.862 AC: 4450 AN: 5164

South Asian (SAS) AF: 0.740 AC: 3562 AN: 4816

European-Finnish (FIN) AF: 0.850 AC: 9008 AN: 10592

Middle Eastern (MID) AF: 0.753 AC: 220 AN: 292

European-Non Finnish (NFE) AF: 0.804 AC: 54700 AN: 68012

Other (OTH) AF: 0.687 AC: 1445 AN: 2104

Alfa AF: 0.771 Hom.: 21524

Bravo AF: 0.625

Asia WGS AF: 0.749 AC: 2604 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	3.5
DANN	Benign	0.59
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs6107905; hg19: chr20-6979153;