rs4972803

Positions:

• chr2-176112386-G-A
• chr2-176112386-G-C
• chr2-176112386-G-T

Variant summary

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

The XR_007073114.1(HOXD11):​n.2313G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,208 control chromosomes in the GnomAD database, including 1,475 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 0.12 (1475 hom., cov: 33)
• Consequence: HOXD11 XR_007073114.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.323

Genes affected

HOXD11 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HOXD11	XR_007073114.1	n.2313G>A		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HOXD10	ENST00000490088.2	n.569+3028G>A		intron_variant		2
HOXD10	ENST00000549469.1	n.616+870G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18913 AN: 152090 Hom.: 1474 Cov.: 33

Gnomad AFR AF: 0.0479

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.0100

Gnomad SAS AF: 0.0944

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.124 AC: 18920 AN: 152208 Hom.: 1475 Cov.: 33 AF XY: 0.124 AC XY: 9197 AN XY: 74418

Gnomad4 AFR AF: 0.0478

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.0101

Gnomad4 SAS AF: 0.0943

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.105

Alfa AF: 0.0898 Hom.: 177

Bravo AF: 0.119

Asia WGS AF: 0.0600 AC: 210 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.5
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4972803; hg19: chr2-176977114;