rs6668

chr7-27098564-C-T

Variant summary

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

The NR_038366.1(HOTAIRM1):n.296-534C>T 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 0.272 in 152,174 control chromosomes in the GnomAD database, including 7,247 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 0.27 (7247 hom., cov: 33)
• Consequence: HOTAIRM1 NR_038366.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.119

Genes affected

HOTAIRM1 (HGNC:37117): (HOXA transcript antisense RNA, myeloid-specific 1) This non-coding locus is located in the HOX gene cluster. Transcription of this locus is induced by retinoic acid, and transcripts likely function in regulation of myelopoiesis through transcriptional activation of several genes in the HOXA cluster, in addition to several beta-2 integrins. [provided by RefSeq, Jan 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HOTAIRM1	NR_038366.1	n.296-534C>T		intron_variant, non_coding_transcript_variant
HOTAIRM1	NR_038367.1	n.296-1215C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HOTAIRM1	ENST00000429611.7	n.266-534C>T		intron_variant, non_coding_transcript_variant		1
HOTAIRM1	ENST00000434063.3	n.296-1215C>T		intron_variant, non_coding_transcript_variant		1
HOTAIRM1	ENST00000425358.2	n.157-510C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41422 AN: 152056 Hom.: 7248 Cov.: 33

Gnomad AFR AF: 0.0678

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.0839

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.272 AC: 41419 AN: 152174 Hom.: 7247 Cov.: 33 AF XY: 0.274 AC XY: 20372 AN XY: 74398

Gnomad4 AFR AF: 0.0676

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.447

Gnomad4 EAS AF: 0.0843

Gnomad4 SAS AF: 0.256

Gnomad4 FIN AF: 0.376

Gnomad4 NFE AF: 0.370

Gnomad4 OTH AF: 0.295

Alfa AF: 0.333 Hom.: 1941

Bravo AF: 0.260

Asia WGS AF: 0.171 AC: 598 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
Cadd	Benign	11
Dann	Benign	0.95

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6668; hg19: chr7-27138183;