rs2747442

Variant names:

• chr6-29685409-A-G
• rs2747442

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 0.349 in 151,948 control chromosomes in the GnomAD database, including 9,760 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 0.35 (9760 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.200
• Publications: 20 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.415 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: 0.349 AC: 53008 AN: 151830 Hom.: 9748 Cov.: 31

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.349 AC: 53057 AN: 151948 Hom.: 9760 Cov.: 31 AF XY: 0.347 AC XY: 25790 AN XY: 74278

African (AFR) AF: 0.420 AC: 17393 AN: 41414

American (AMR) AF: 0.421 AC: 6424 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.463 AC: 1605 AN: 3464

East Asian (EAS) AF: 0.245 AC: 1265 AN: 5166

South Asian (SAS) AF: 0.360 AC: 1729 AN: 4804

European-Finnish (FIN) AF: 0.200 AC: 2108 AN: 10546

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.314 AC: 21358 AN: 67982

Other (OTH) AF: 0.389 AC: 819 AN: 2106

Alfa AF: 0.330 Hom.: 21924

Bravo AF: 0.372

Asia WGS AF: 0.256 AC: 892 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.7
DANN	Benign	0.31
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs2747442; hg19: chr6-29653186;