chr2-172425667-T-C

Position:

• chr2-172425667-T-C

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 0.826 in 152,158 control chromosomes in the GnomAD database, including 52,027 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 0.83 (52027 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.745

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.888 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.172425667T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.826 AC: 125591 AN: 152040 Hom.: 51987 Cov.: 32

Gnomad AFR AF: 0.827

Gnomad AMI AF: 0.782

Gnomad AMR AF: 0.854

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.909

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.872

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.824

Gnomad OTH AF: 0.815

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

GnomAD4 genome AF: 0.826 AC: 125684 AN: 152158 Hom.: 52027 Cov.: 32 AF XY: 0.826 AC XY: 61418 AN XY: 74398

Gnomad4 AFR AF: 0.827

Gnomad4 AMR AF: 0.854

Gnomad4 ASJ AF: 0.704

Gnomad4 EAS AF: 0.909

Gnomad4 SAS AF: 0.672

Gnomad4 FIN AF: 0.872

Gnomad4 NFE AF: 0.824

Gnomad4 OTH AF: 0.812

Alfa AF: 0.814 Hom.: 75926

Bravo AF: 0.830

Asia WGS AF: 0.808 AC: 2813 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.5
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2141698; hg19: chr2-173290395;