rs4674257

Variant names:

• chr2-218124051-A-G
• rs4674257

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 0.599 in 151,850 control chromosomes in the GnomAD database, including 28,467 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 0.60 (28467 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.525
• Publications: 20 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.776 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: 0.599 AC: 90826 AN: 151732 Hom.: 28435 Cov.: 31

Gnomad AFR AF: 0.783

Gnomad AMI AF: 0.727

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.653

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.599 AC: 90896 AN: 151850 Hom.: 28467 Cov.: 31 AF XY: 0.594 AC XY: 44088 AN XY: 74210

African (AFR) AF: 0.783 AC: 32430 AN: 41414

American (AMR) AF: 0.564 AC: 8598 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.653 AC: 2264 AN: 3466

East Asian (EAS) AF: 0.360 AC: 1862 AN: 5172

South Asian (SAS) AF: 0.607 AC: 2927 AN: 4822

European-Finnish (FIN) AF: 0.432 AC: 4534 AN: 10494

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.531 AC: 36095 AN: 67926

Other (OTH) AF: 0.621 AC: 1308 AN: 2106

Alfa AF: 0.559 Hom.: 39670

Bravo AF: 0.612

Asia WGS AF: 0.493 AC: 1715 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.9
DANN	Benign	0.67
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs4674257; hg19: chr2-218988774;