rs4675690

Variant names:

• chr2-207643083-C-T
• rs4675690

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 0.48 in 151,766 control chromosomes in the GnomAD database, including 17,660 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 0.48 (17660 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.220
• Publications: 24 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.591 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: 0.480 AC: 72841 AN: 151648 Hom.: 17648 Cov.: 30

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.480 AC: 72887 AN: 151766 Hom.: 17660 Cov.: 30 AF XY: 0.482 AC XY: 35727 AN XY: 74148

African (AFR) AF: 0.512 AC: 21200 AN: 41368

American (AMR) AF: 0.474 AC: 7220 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.517 AC: 1794 AN: 3470

East Asian (EAS) AF: 0.608 AC: 3120 AN: 5128

South Asian (SAS) AF: 0.427 AC: 2050 AN: 4802

European-Finnish (FIN) AF: 0.478 AC: 5021 AN: 10510

Middle Eastern (MID) AF: 0.507 AC: 148 AN: 292

European-Non Finnish (NFE) AF: 0.455 AC: 30923 AN: 67930

Other (OTH) AF: 0.505 AC: 1066 AN: 2112

Alfa AF: 0.469 Hom.: 47225

Bravo AF: 0.481

Asia WGS AF: 0.518 AC: 1800 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.6
DANN	Benign	0.78
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs4675690; hg19: chr2-208507807;