chr6-51020055-A-G

Variant names:

• chr6-51020055-A-G
• rs190759

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 0.84 in 152,192 control chromosomes in the GnomAD database, including 53,978 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 0.84 (53978 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.966 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: 0.840 AC: 127779 AN: 152074 Hom.: 53950 Cov.: 32

Gnomad AFR AF: 0.851

Gnomad AMI AF: 0.785

Gnomad AMR AF: 0.843

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.989

Gnomad SAS AF: 0.842

Gnomad FIN AF: 0.904

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.840 AC: 127861 AN: 152192 Hom.: 53978 Cov.: 32 AF XY: 0.845 AC XY: 62841 AN XY: 74400

African (AFR) AF: 0.850 AC: 35305 AN: 41512

American (AMR) AF: 0.843 AC: 12889 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.681 AC: 2362 AN: 3470

East Asian (EAS) AF: 0.989 AC: 5114 AN: 5172

South Asian (SAS) AF: 0.841 AC: 4050 AN: 4818

European-Finnish (FIN) AF: 0.904 AC: 9586 AN: 10604

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.823 AC: 55984 AN: 68012

Other (OTH) AF: 0.794 AC: 1674 AN: 2108

Alfa AF: 0.823 Hom.: 141264

Bravo AF: 0.837

Asia WGS AF: 0.905 AC: 3145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	14
DANN	Benign	0.72
PhyloP100		-0.080

Splicing

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

Other links and lift over

dbSNP: rs190759; hg19: chr6-50987768;