rs6668

Positions:

• chr7-27098564-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

HOTAIRM1 (HGNC:):

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	Protein	UniProt
HOTAIRM1	NR_038366.1	n.296-534C>T		intron_variant
HOTAIRM1	NR_038367.1	n.296-1215C>T		intron_variant

Ensembl

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