chr2-4675608-T-C

Variant names:

• chr2-4675608-T-C
• rs285540

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 0.85 in 152,252 control chromosomes in the GnomAD database, including 55,320 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 0.85 (55320 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.935 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: 0.850 AC: 129255 AN: 152136 Hom.: 55271 Cov.: 34

Gnomad AFR AF: 0.943

Gnomad AMI AF: 0.642

Gnomad AMR AF: 0.889

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.806

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.815

Gnomad OTH AF: 0.840

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

GnomAD4 genome AF: 0.850 AC: 129362 AN: 152252 Hom.: 55320 Cov.: 34 AF XY: 0.847 AC XY: 63053 AN XY: 74418

African (AFR) AF: 0.943 AC: 39199 AN: 41584

American (AMR) AF: 0.889 AC: 13603 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.704 AC: 2443 AN: 3472

East Asian (EAS) AF: 0.752 AC: 3866 AN: 5138

South Asian (SAS) AF: 0.764 AC: 3687 AN: 4826

European-Finnish (FIN) AF: 0.806 AC: 8547 AN: 10604

Middle Eastern (MID) AF: 0.805 AC: 235 AN: 292

European-Non Finnish (NFE) AF: 0.815 AC: 55427 AN: 68014

Other (OTH) AF: 0.839 AC: 1771 AN: 2110

Alfa AF: 0.782 Hom.: 2575

Bravo AF: 0.861

Asia WGS AF: 0.735 AC: 2555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.54
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs285540; hg19: chr2-4723198;