rs2113563

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr2-176134284-A-G
• chr2-176134284-A-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HOXD-AS2	ENST00000440016.6	n.497+1035T>C		intron_variant	Intron 2 of 3	5
HOXD-AS2	ENST00000651440.1	n.251+1035T>C		intron_variant	Intron 2 of 2

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;