20-7658056-A-G

Variant names:

• chr20-7658056-A-G
• rs6086149

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 0.268 in 150,636 control chromosomes in the GnomAD database, including 6,133 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 0.27 (6133 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.433
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.379 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: 0.268 AC: 40408 AN: 150526 Hom.: 6128 Cov.: 31

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.268 AC: 40421 AN: 150636 Hom.: 6133 Cov.: 31 AF XY: 0.267 AC XY: 19697 AN XY: 73660

African (AFR) AF: 0.125 AC: 5073 AN: 40466

American (AMR) AF: 0.388 AC: 5881 AN: 15174

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1156 AN: 3458

East Asian (EAS) AF: 0.238 AC: 1230 AN: 5160

South Asian (SAS) AF: 0.282 AC: 1360 AN: 4818

European-Finnish (FIN) AF: 0.257 AC: 2708 AN: 10552

Middle Eastern (MID) AF: 0.390 AC: 114 AN: 292

European-Non Finnish (NFE) AF: 0.324 AC: 21954 AN: 67704

Other (OTH) AF: 0.307 AC: 646 AN: 2102

Alfa AF: 0.303 Hom.: 20683

Bravo AF: 0.274

Asia WGS AF: 0.286 AC: 994 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.2
DANN	Benign	0.76
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs6086149; hg19: chr20-7638703;