2-176127051-A-G

Variant names:

• chr2-176127051-A-G
• rs2592394
• ENST00000440016.6:n.498-4607T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000440016.6(HOXD-AS2):​n.498-4607T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.734 in 152,120 control chromosomes in the GnomAD database, including 41,349 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 0.73 (41349 hom., cov: 32)
• Consequence: HOXD-AS2 ENST00000440016.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.805 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HOXD-AS2	ENST00000440016.6	n.498-4607T>C		intron_variant	Intron 2 of 3	5

Frequencies

GnomAD3 genomes AF: 0.734 AC: 111574 AN: 152002 Hom.: 41312 Cov.: 32

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.762

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.436

Gnomad SAS AF: 0.753

Gnomad FIN AF: 0.750

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.730

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

GnomAD4 genome AF: 0.734 AC: 111667 AN: 152120 Hom.: 41349 Cov.: 32 AF XY: 0.736 AC XY: 54701 AN XY: 74344

Gnomad4 AFR AF: 0.812

Gnomad4 AMR AF: 0.763

Gnomad4 ASJ AF: 0.709

Gnomad4 EAS AF: 0.436

Gnomad4 SAS AF: 0.754

Gnomad4 FIN AF: 0.750

Gnomad4 NFE AF: 0.700

Gnomad4 OTH AF: 0.728

Alfa AF: 0.702 Hom.: 56257

Bravo AF: 0.736

Asia WGS AF: 0.611 AC: 2129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2592394; hg19: chr2-176991779;