2-75041676-T-C

Variant names:

• chr2-75041676-T-C
• rs4614953

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 0.739 in 152,172 control chromosomes in the GnomAD database, including 41,941 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 0.74 (41941 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.451
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.805 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.739 AC: 112388 AN: 152054 Hom.: 41899 Cov.: 34

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.764

Gnomad AMR AF: 0.754

Gnomad ASJ AF: 0.815

Gnomad EAS AF: 0.748

Gnomad SAS AF: 0.731

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.710

Gnomad OTH AF: 0.752

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

GnomAD4 genome AF: 0.739 AC: 112488 AN: 152172 Hom.: 41941 Cov.: 34 AF XY: 0.735 AC XY: 54704 AN XY: 74396

African (AFR) AF: 0.812 AC: 33730 AN: 41532

American (AMR) AF: 0.754 AC: 11516 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.815 AC: 2830 AN: 3472

East Asian (EAS) AF: 0.748 AC: 3875 AN: 5182

South Asian (SAS) AF: 0.732 AC: 3527 AN: 4820

European-Finnish (FIN) AF: 0.590 AC: 6231 AN: 10562

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.709 AC: 48249 AN: 68008

Other (OTH) AF: 0.750 AC: 1585 AN: 2112

Alfa AF: 0.727 Hom.: 53449

Bravo AF: 0.751

Asia WGS AF: 0.723 AC: 2516 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.4
DANN	Benign	0.76
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs4614953; hg19: chr2-75268803;