rs268172

chr2-175207178-A-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	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

Gnomad4 AFR AF: 0.561

Gnomad4 AMR AF: 0.745

Gnomad4 ASJ AF: 0.803

Gnomad4 EAS AF: 0.863

Gnomad4 SAS AF: 0.803

Gnomad4 FIN AF: 0.884

Gnomad4 NFE AF: 0.822

Gnomad4 OTH AF: 0.746

Alfa AF: 0.774 Hom.: 5768

Bravo AF: 0.725

Asia WGS AF: 0.807 AC: 2808 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
Cadd	Benign	12
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs268172; hg19: chr2-176071906;