rs6739054

Variant names:

• chr2-11080436-A-G
• rs6739054

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 0.267 in 152,020 control chromosomes in the GnomAD database, including 6,501 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 (6501 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.304
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.42 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: 0.267 AC: 40555 AN: 151902 Hom.: 6501 Cov.: 31

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.450

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.419

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.267 AC: 40565 AN: 152020 Hom.: 6501 Cov.: 31 AF XY: 0.281 AC XY: 20842 AN XY: 74284

African (AFR) AF: 0.105 AC: 4360 AN: 41502

American (AMR) AF: 0.329 AC: 5021 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 973 AN: 3472

East Asian (EAS) AF: 0.420 AC: 2156 AN: 5136

South Asian (SAS) AF: 0.436 AC: 2100 AN: 4820

European-Finnish (FIN) AF: 0.483 AC: 5103 AN: 10562

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.292 AC: 19823 AN: 67930

Other (OTH) AF: 0.254 AC: 536 AN: 2114

Alfa AF: 0.279 Hom.: 27651

Bravo AF: 0.246

Asia WGS AF: 0.422 AC: 1468 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.86
DANN	Benign	0.58
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs6739054; hg19: chr2-11220562;