rs564053

Variant names:

• chr6-94108276-A-G
• rs564053

Your query was ambiguous. Multiple possible variants found:

• chr6-94108276-A-G
• chr6-94108276-A-T

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 0.819 in 151,716 control chromosomes in the GnomAD database, including 51,071 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 0.82 (51071 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.919 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: 0.819 AC: 124116 AN: 151598 Hom.: 51011 Cov.: 30

Gnomad AFR AF: 0.838

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.850

Gnomad ASJ AF: 0.794

Gnomad EAS AF: 0.941

Gnomad SAS AF: 0.796

Gnomad FIN AF: 0.892

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.782

Gnomad OTH AF: 0.794

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

GnomAD4 genome AF: 0.819 AC: 124236 AN: 151716 Hom.: 51071 Cov.: 30 AF XY: 0.827 AC XY: 61306 AN XY: 74118

African (AFR) AF: 0.838 AC: 34702 AN: 41392

American (AMR) AF: 0.850 AC: 12920 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.794 AC: 2752 AN: 3466

East Asian (EAS) AF: 0.941 AC: 4784 AN: 5082

South Asian (SAS) AF: 0.796 AC: 3829 AN: 4810

European-Finnish (FIN) AF: 0.892 AC: 9429 AN: 10576

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.782 AC: 53107 AN: 67876

Other (OTH) AF: 0.796 AC: 1680 AN: 2110

Alfa AF: 0.798 Hom.: 91389

Bravo AF: 0.818

Asia WGS AF: 0.826 AC: 2870 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.31
DANN	Benign	0.29
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs564053; hg19: chr6-94817994;