chr7-27098564-C-T

Variant names:

• chr7-27098564-C-T
• rs6668
• ENST00000429611.7:n.266-534C>T

Variant summary

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

The ENST00000429611.7(HOTAIRM1):​n.266-534C>T variant causes a intron 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 ENST00000429611.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.119
• Publications: 13 publications found

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]

ENSG00000293629 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
HOTAIRM1	NR_038366.1	n.296-534C>T		intron_variant	Intron 1 of 2
HOTAIRM1	NR_038367.1	n.296-1215C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HOTAIRM1	ENST00000429611.7	n.266-534C>T		intron_variant	Intron 1 of 2	1
HOTAIRM1	ENST00000434063.3	n.296-1215C>T		intron_variant	Intron 1 of 1	1
HOTAIRM1	ENST00000425358.2	n.157-510C>T		intron_variant	Intron 1 of 2	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

African (AFR) AF: 0.0676 AC: 2808 AN: 41566

American (AMR) AF: 0.342 AC: 5235 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.447 AC: 1552 AN: 3472

East Asian (EAS) AF: 0.0843 AC: 435 AN: 5158

South Asian (SAS) AF: 0.256 AC: 1235 AN: 4824

European-Finnish (FIN) AF: 0.376 AC: 3978 AN: 10584

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.370 AC: 25138 AN: 67968

Other (OTH) AF: 0.295 AC: 624 AN: 2112

Alfa AF: 0.282 Hom.: 4453

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
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs6668; hg19: chr7-27138183;