rs2592394

chr2-176127051-A-G

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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HOXD-AS2	ENST00000440016.6	n.498-4607T>C		intron_variant, non_coding_transcript_variant		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;