chr2-175182134-C-A

Position:

• chr2-175182134-C-A

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 0.752 in 152,100 control chromosomes in the GnomAD database, including 43,754 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 (43738 hom., cov: 31)
  • Exomes 𝑓: 0.86 (16 hom.)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.841 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.175182134C>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.752 AC: 114322 AN: 151940 Hom.: 43710 Cov.: 31

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.886

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.766

Gnomad EAS AF: 0.862

Gnomad SAS AF: 0.808

Gnomad FIN AF: 0.883

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.816

Gnomad OTH AF: 0.744

GnomAD4 exome AF: 0.857 AC: 36 AN: 42 Hom.: 16 Cov.: 0 AF XY: 0.861 AC XY: 31 AN XY: 36

Gnomad4 AFR exome AF: 1.00

Gnomad4 ASJ exome AF: 0.750

Gnomad4 EAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.958

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.752 AC: 114391 AN: 152058 Hom.: 43738 Cov.: 31 AF XY: 0.756 AC XY: 56209 AN XY: 74326

Gnomad4 AFR AF: 0.594

Gnomad4 AMR AF: 0.745

Gnomad4 ASJ AF: 0.766

Gnomad4 EAS AF: 0.862

Gnomad4 SAS AF: 0.809

Gnomad4 FIN AF: 0.883

Gnomad4 NFE AF: 0.816

Gnomad4 OTH AF: 0.747

Alfa AF: 0.767 Hom.: 6610

Bravo AF: 0.732

Asia WGS AF: 0.818 AC: 2844 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.27
DANN	Benign	0.81

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs268230; hg19: chr2-176046862;