2-175207178-A-G

Variant names:

• chr2-175207178-A-G
• rs268172

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 0.747 in 152,026 control chromosomes in the GnomAD database, including 43,455 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 0.75 (43455 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.623
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.842 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: 0.747 AC: 113518 AN: 151912 Hom.: 43430 Cov.: 31

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.905

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.803

Gnomad EAS AF: 0.864

Gnomad SAS AF: 0.802

Gnomad FIN AF: 0.884

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.822

Gnomad OTH AF: 0.743

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

GnomAD4 genome AF: 0.747 AC: 113576 AN: 152026 Hom.: 43455 Cov.: 31 AF XY: 0.750 AC XY: 55737 AN XY: 74306

African (AFR) AF: 0.561 AC: 23251 AN: 41412

American (AMR) AF: 0.745 AC: 11377 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.803 AC: 2784 AN: 3468

East Asian (EAS) AF: 0.863 AC: 4455 AN: 5162

South Asian (SAS) AF: 0.803 AC: 3873 AN: 4822

European-Finnish (FIN) AF: 0.884 AC: 9363 AN: 10586

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.822 AC: 55862 AN: 67990

Other (OTH) AF: 0.746 AC: 1576 AN: 2112

Alfa AF: 0.767 Hom.: 5904

Bravo AF: 0.725

Asia WGS AF: 0.807 AC: 2808 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	12
DANN	Benign	0.77
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs268172; hg19: chr2-176071906;