rs983186

Variant names:

• chr7-27149040-G-A
• rs983186
• NM_153631.3:c.-494+3248C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-27149040-G-A
• chr7-27149040-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_153631.3(HOXA3):​c.-494+3248C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.583 in 152,216 control chromosomes in the GnomAD database, including 30,840 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 0.58 (30840 hom., cov: 34)
• Consequence: HOXA3 NM_153631.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08
• Publications: 13 publications found

Genes affected

HOXA3 (HGNC:5104): (homeobox A3) In vertebrates, the genes encoding the class of transcription factors called homeobox genes are found in clusters named A, B, C, and D on four separate chromosomes. Expression of these proteins is spatially and temporally regulated during embryonic development. This gene is part of the A cluster on chromosome 7 and encodes a DNA-binding transcription factor which may regulate gene expression, morphogenesis, and differentiation. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ENSG00000272801 (HGNC:):

HOXA-AS3 (HGNC:43748): (HOXA cluster antisense RNA 3)

HOXA6 (HGNC:5107): (homeobox A6) In vertebrates, the genes encoding the class of transcription factors called homeobox genes are found in clusters named A, B, C, and D on four separate chromosomes. Expression of these proteins is spatially and temporally regulated during embryonic development. This gene is part of the A cluster on chromosome 7 and encodes a DNA-binding transcription factor which may regulate gene expression, morphogenesis, and differentiation. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_153631.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HOXA3	NM_153631.3	MANE Select	c.-494+3248C>T		intron	N/A	NP_705895.1	O43365
	HOXA3	NM_001384335.1		c.-610+3248C>T		intron	N/A	NP_001371264.1	O43365
	HOXA3	NM_001384336.1		c.-309+1268C>T		intron	N/A	NP_001371265.1	O43365

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HOXA3	ENST00000612286.5	TSL:2 MANE Select	c.-494+3248C>T		intron	N/A	ENSP00000484411.1	O43365
	ENSG00000272801	ENST00000498652.1	TSL:1	n.312-1618C>T		intron	N/A
	HOXA3	ENST00000851228.1		c.-309+3248C>T		intron	N/A	ENSP00000521287.1

Frequencies

GnomAD3 genomes AF: 0.583 AC: 88675 AN: 152098 Hom.: 30841 Cov.: 34

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.815

Gnomad EAS AF: 0.633

Gnomad SAS AF: 0.769

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.637

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

GnomAD4 genome AF: 0.583 AC: 88689 AN: 152216 Hom.: 30840 Cov.: 34 AF XY: 0.583 AC XY: 43410 AN XY: 74426

African (AFR) AF: 0.181 AC: 7514 AN: 41556

American (AMR) AF: 0.637 AC: 9746 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.815 AC: 2830 AN: 3472

East Asian (EAS) AF: 0.633 AC: 3259 AN: 5146

South Asian (SAS) AF: 0.769 AC: 3715 AN: 4830

European-Finnish (FIN) AF: 0.703 AC: 7450 AN: 10602

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.765 AC: 52005 AN: 68004

Other (OTH) AF: 0.637 AC: 1344 AN: 2110

Alfa AF: 0.716 Hom.: 67882

Bravo AF: 0.556

Asia WGS AF: 0.665 AC: 2313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.8
DANN	Benign	0.91
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs983186; hg19: chr7-27188659;