chr7-155068597-A-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

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

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000395731.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HTR5A-AS1	NR_038945.1		n.1173T>G		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HTR5A-AS1	ENST00000395731.5	TSL:1	n.1173T>G		non_coding_transcript_exon	Exon 2 of 2
	HTR5A-AS1	ENST00000655797.2		n.1498T>G		non_coding_transcript_exon	Exon 3 of 3
	HTR5A-AS1	ENST00000671665.1		n.2066T>G		non_coding_transcript_exon	Exon 2 of 2

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.348 AC: 14454 AN: 41482

American (AMR) AF: 0.284 AC: 4343 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 766 AN: 3466

East Asian (EAS) AF: 0.582 AC: 3009 AN: 5170

South Asian (SAS) AF: 0.262 AC: 1261 AN: 4818

European-Finnish (FIN) AF: 0.283 AC: 2988 AN: 10572

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.278 AC: 18890 AN: 67996

Other (OTH) AF: 0.289 AC: 608 AN: 2106

Alfa AF: 0.263 Hom.: 2841

Bravo AF: 0.313

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	5.1
DANN	Benign	0.86
PhyloP100		0.59
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1017488;

hg19: chr7-154860307;