2-175052187-T-C

Variant names:

• chr2-175052187-T-C
• rs4972738

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 0.563 in 151,818 control chromosomes in the GnomAD database, including 24,877 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 0.56 (24877 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.625
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.637 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: 0.564 AC: 85498 AN: 151698 Hom.: 24869 Cov.: 31

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.576

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

GnomAD4 genome AF: 0.563 AC: 85532 AN: 151818 Hom.: 24877 Cov.: 31 AF XY: 0.564 AC XY: 41881 AN XY: 74194

African (AFR) AF: 0.422 AC: 17469 AN: 41384

American (AMR) AF: 0.501 AC: 7648 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.579 AC: 2008 AN: 3470

East Asian (EAS) AF: 0.551 AC: 2835 AN: 5144

South Asian (SAS) AF: 0.609 AC: 2932 AN: 4812

European-Finnish (FIN) AF: 0.664 AC: 7011 AN: 10558

Middle Eastern (MID) AF: 0.606 AC: 177 AN: 292

European-Non Finnish (NFE) AF: 0.642 AC: 43572 AN: 67890

Other (OTH) AF: 0.575 AC: 1208 AN: 2102

Alfa AF: 0.626 Hom.: 15001

Bravo AF: 0.543

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.3
DANN	Benign	0.74
PhyloP100		0.63

Splicing

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

Other links and lift over

dbSNP: rs4972738; hg19: chr2-175916915;