2-176134284-A-G

Position:

• chr2-176134284-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.531 in 152,172 control chromosomes in the GnomAD database, including 24,737 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 0.53 (24737 hom., cov: 34)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.48

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.27).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.176134284A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HOXD-AS2	ENST00000440016.6	n.497+1035T>C		intron_variant		5
HOXD-AS2	ENST00000651440.1	n.251+1035T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80842 AN: 152054 Hom.: 24724 Cov.: 34

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.762

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.555

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

GnomAD4 genome AF: 0.531 AC: 80875 AN: 152172 Hom.: 24737 Cov.: 34 AF XY: 0.538 AC XY: 40033 AN XY: 74400

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.659

Gnomad4 ASJ AF: 0.617

Gnomad4 EAS AF: 0.346

Gnomad4 SAS AF: 0.671

Gnomad4 FIN AF: 0.722

Gnomad4 NFE AF: 0.664

Gnomad4 OTH AF: 0.556

Alfa AF: 0.643 Hom.: 49549

Bravo AF: 0.510

Asia WGS AF: 0.486 AC: 1695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.27
CADD	Benign	21
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2113563; hg19: chr2-176999012;