rs2698501

Variant names:

• chr7-155068981-A-G
• rs2698501
• ENST00000395731.5:n.789T>C

Variant summary

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

The ENST00000395731.5(HTR5A-AS1):​n.789T>C 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 0.264 in 229,730 control chromosomes in the GnomAD database, including 8,543 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 (5855 hom., cov: 33)
  • Exomes 𝑓: 0.25 (2688 hom.)
• Consequence: HTR5A-AS1 ENST00000395731.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.86

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HTR5A-AS1	NR_038945.1	n.789T>C		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.789T>C		non_coding_transcript_exon_variant	Exon 2 of 2	1
HTR5A-AS1	ENST00000493904.3	n.816T>C		non_coding_transcript_exon_variant	Exon 2 of 2	4
HTR5A-AS1	ENST00000655797.1	n.1114T>C		non_coding_transcript_exon_variant	Exon 3 of 3
HTR5A-AS1	ENST00000671665.1	n.1682T>C		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41507 AN: 152000 Hom.: 5852 Cov.: 33

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.260

GnomAD4 exome AF: 0.245 AC: 19037 AN: 77612 Hom.: 2688 Cov.: 0 AF XY: 0.245 AC XY: 10382 AN XY: 42404

Gnomad4 AFR exome AF: 0.242

Gnomad4 AMR exome AF: 0.191

Gnomad4 ASJ exome AF: 0.206

Gnomad4 EAS exome AF: 0.396

Gnomad4 SAS exome AF: 0.226

Gnomad4 FIN exome AF: 0.237

Gnomad4 NFE exome AF: 0.251

Gnomad4 OTH exome AF: 0.242

GnomAD4 genome AF: 0.273 AC: 41524 AN: 152118 Hom.: 5855 Cov.: 33 AF XY: 0.272 AC XY: 20260 AN XY: 74378

Gnomad4 AFR AF: 0.269

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.231

Gnomad4 EAS AF: 0.424

Gnomad4 SAS AF: 0.259

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.277

Gnomad4 OTH AF: 0.259

Alfa AF: 0.268 Hom.: 1210

Bravo AF: 0.271

Asia WGS AF: 0.306 AC: 1064 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.3
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2698501; hg19: chr7-154860691;