rs1859164

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000396344.4(HOXA10):​c.10+846A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 152,032 control chromosomes in the GnomAD database, including 12,643 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 0.39 ( 12643 hom., cov: 33)

Consequence

HOXA10
ENST00000396344.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.27
Variant links:
Genes affected
HOXA10 (HGNC:5100): (homeobox A10) 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 that may regulate gene expression, morphogenesis, and differentiation. More specifically, it may function in fertility, embryo viability, and regulation of hematopoietic lineage commitment. Alternatively spliced transcript variants have been described. Read-through transcription also exists between this gene and the downstream homeobox A9 (HOXA9) gene. [provided by RefSeq, Mar 2011]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.517 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
HOXA10-HOXA9NR_037940.1 linkuse as main transcriptn.616+846A>G intron_variant, non_coding_transcript_variant
HOXA10NR_037939.2 linkuse as main transcriptn.216+846A>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
HOXA10ENST00000396344.4 linkuse as main transcriptc.10+846A>G intron_variant 1 A1P31260-2

Frequencies

GnomAD3 genomes
AF:
0.389
AC:
59046
AN:
151912
Hom.:
12644
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.203
Gnomad AMI
AF:
0.480
Gnomad AMR
AF:
0.388
Gnomad ASJ
AF:
0.504
Gnomad EAS
AF:
0.534
Gnomad SAS
AF:
0.498
Gnomad FIN
AF:
0.441
Gnomad MID
AF:
0.497
Gnomad NFE
AF:
0.466
Gnomad OTH
AF:
0.431
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.389
AC:
59068
AN:
152032
Hom.:
12643
Cov.:
33
AF XY:
0.389
AC XY:
28921
AN XY:
74334
show subpopulations
Gnomad4 AFR
AF:
0.203
Gnomad4 AMR
AF:
0.388
Gnomad4 ASJ
AF:
0.504
Gnomad4 EAS
AF:
0.534
Gnomad4 SAS
AF:
0.499
Gnomad4 FIN
AF:
0.441
Gnomad4 NFE
AF:
0.466
Gnomad4 OTH
AF:
0.435
Alfa
AF:
0.284
Hom.:
770
Bravo
AF:
0.377
Asia WGS
AF:
0.484
AC:
1686
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
1.6
DANN
Benign
0.61

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1859164; hg19: chr7-27218419; API