rs2857154

Variant names:

• chr6-32794839-A-G
• rs2857154

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 0.673 in 152,090 control chromosomes in the GnomAD database, including 34,646 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 0.67 (34646 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.801
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.787 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: 0.673 AC: 102260 AN: 151972 Hom.: 34637 Cov.: 31

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.822

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.719

Gnomad SAS AF: 0.809

Gnomad FIN AF: 0.768

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.680

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

GnomAD4 genome AF: 0.673 AC: 102306 AN: 152090 Hom.: 34646 Cov.: 31 AF XY: 0.680 AC XY: 50509 AN XY: 74326

African (AFR) AF: 0.651 AC: 26986 AN: 41450

American (AMR) AF: 0.656 AC: 10038 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.708 AC: 2457 AN: 3468

East Asian (EAS) AF: 0.719 AC: 3719 AN: 5176

South Asian (SAS) AF: 0.808 AC: 3899 AN: 4824

European-Finnish (FIN) AF: 0.768 AC: 8131 AN: 10584

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.657 AC: 44655 AN: 67976

Other (OTH) AF: 0.683 AC: 1442 AN: 2112

Alfa AF: 0.658 Hom.: 12640

Bravo AF: 0.659

Asia WGS AF: 0.749 AC: 2607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.7
DANN	Benign	0.33
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs2857154; hg19: chr6-32762616;