rs1774886

Variant names:

• chr20-6147576-G-A
• rs1774886

Your query was ambiguous. Multiple possible variants found:

• chr20-6147576-G-A
• chr20-6147576-G-C

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 0.813 in 152,118 control chromosomes in the GnomAD database, including 50,359 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 0.81 (50359 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0200
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.862 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.813 AC: 123617 AN: 152000 Hom.: 50313 Cov.: 32

Gnomad AFR AF: 0.783

Gnomad AMI AF: 0.908

Gnomad AMR AF: 0.858

Gnomad ASJ AF: 0.800

Gnomad EAS AF: 0.883

Gnomad SAS AF: 0.795

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.824

Gnomad OTH AF: 0.800

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

GnomAD4 genome AF: 0.813 AC: 123721 AN: 152118 Hom.: 50359 Cov.: 32 AF XY: 0.812 AC XY: 60338 AN XY: 74350

African (AFR) AF: 0.783 AC: 32473 AN: 41474

American (AMR) AF: 0.858 AC: 13128 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.800 AC: 2777 AN: 3470

East Asian (EAS) AF: 0.884 AC: 4573 AN: 5174

South Asian (SAS) AF: 0.794 AC: 3821 AN: 4810

European-Finnish (FIN) AF: 0.772 AC: 8180 AN: 10590

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.824 AC: 56030 AN: 67998

Other (OTH) AF: 0.800 AC: 1685 AN: 2106

Alfa AF: 0.822 Hom.: 166207

Bravo AF: 0.818

Asia WGS AF: 0.862 AC: 2996 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.34
PhyloP100		0.020

Splicing

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

Other links and lift over

dbSNP: rs1774886; hg19: chr20-6128223;