rs4675690

Positions:

• chr2-207643083-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;