rs4675690

Variant names:

• chr2-207643083-C-T
• rs4675690

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.512

Gnomad4 AMR AF: 0.474

Gnomad4 ASJ AF: 0.517

Gnomad4 EAS AF: 0.608

Gnomad4 SAS AF: 0.427

Gnomad4 FIN AF: 0.478

Gnomad4 NFE AF: 0.455

Gnomad4 OTH AF: 0.505

Alfa AF: 0.467 Hom.: 16589

Bravo AF: 0.481

Asia WGS AF: 0.518 AC: 1800 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4675690; hg19: chr2-208507807;