rs1017488

Variant names:

• chr7-155068597-A-C
• rs1017488
• ENST00000395731.5:n.1173T>G

Your query was ambiguous. Multiple possible variants found:

• chr7-155068597-A-C
• chr7-155068597-A-G
• chr7-155068597-A-T

Variant summary

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

The ENST00000395731.5(HTR5A-AS1):​n.1173T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 152,086 control chromosomes in the GnomAD database, including 7,495 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 0.31 (7495 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: HTR5A-AS1 ENST00000395731.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.588

Genes affected

HTR5A-AS1 (HGNC:48956): (HTR5A antisense RNA 1)

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 (EAS) allele frequency at 95% confidence interval = 0.565 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HTR5A-AS1	NR_038945.1	n.1173T>G		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HTR5A-AS1	ENST00000395731.5	n.1173T>G		non_coding_transcript_exon_variant	Exon 2 of 2	1
HTR5A-AS1	ENST00000655797.1	n.1498T>G		non_coding_transcript_exon_variant	Exon 3 of 3
HTR5A-AS1	ENST00000671665.1	n.2066T>G		non_coding_transcript_exon_variant	Exon 2 of 2
HTR5A-AS1	ENST00000493904.3	n.*22T>G		downstream_gene_variant		4

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46689 AN: 151968 Hom.: 7494 Cov.: 33

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.289

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.307 AC: 46726 AN: 152086 Hom.: 7495 Cov.: 33 AF XY: 0.308 AC XY: 22876 AN XY: 74336

Gnomad4 AFR AF: 0.348

Gnomad4 AMR AF: 0.284

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.582

Gnomad4 SAS AF: 0.262

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.278

Gnomad4 OTH AF: 0.289

Alfa AF: 0.258 Hom.: 2352

Bravo AF: 0.313

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	5.1
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1017488; hg19: chr7-154860307;