2-176134284-A-G

Variant names:

• chr2-176134284-A-G
• rs2113563
• ENST00000440016.6:n.497+1035T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000440016.6(HOXD-AS2):​n.497+1035T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: HOXD-AS2 ENST00000440016.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.48
• Publications: 7 publications found

Genes affected

HOXD-AS2 (HGNC:43756): (HOXD cluster antisense RNA 2)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000440016.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HOXD-AS2	ENST00000440016.6	TSL:5	n.497+1035T>C		intron	N/A
	HOXD-AS2	ENST00000651440.1		n.251+1035T>C		intron	N/A
	HOXD-AS2	ENST00000426965.2	TSL:1	n.*148T>C		downstream_gene	N/A

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

African (AFR) AF: 0.213 AC: 8823 AN: 41504

American (AMR) AF: 0.659 AC: 10065 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.617 AC: 2142 AN: 3472

East Asian (EAS) AF: 0.346 AC: 1793 AN: 5176

South Asian (SAS) AF: 0.671 AC: 3236 AN: 4824

European-Finnish (FIN) AF: 0.722 AC: 7643 AN: 10592

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.664 AC: 45158 AN: 68004

Other (OTH) AF: 0.556 AC: 1175 AN: 2114

Alfa AF: 0.613 Hom.: 81205

Bravo AF: 0.510

Asia WGS AF: 0.486 AC: 1695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.27
CADD	Benign	21
DANN	Benign	0.89
PhyloP100		2.5

Splicing

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

Other links and lift over

dbSNP: rs2113563; hg19: chr2-176999012;