ENST00000395731.5:n.525-438T>G

Variant names:

• chr7-155069683-A-C
• rs1881691
• ENST00000395731.5:n.525-438T>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.525-438T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 151,972 control chromosomes in the GnomAD database, including 8,126 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 0.32 (8126 hom., cov: 33)
• Consequence: HTR5A-AS1 ENST00000395731.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.321
• Publications: 3 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HTR5A-AS1	NR_038945.1	n.525-438T>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HTR5A-AS1	ENST00000395731.5	n.525-438T>G		intron_variant	Intron 1 of 1	1
HTR5A-AS1	ENST00000493904.3	n.552-438T>G		intron_variant	Intron 1 of 1	4
HTR5A-AS1	ENST00000655797.2	n.850-438T>G		intron_variant	Intron 2 of 2
HTR5A-AS1	ENST00000671665.1	n.1418-438T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49126 AN: 151854 Hom.: 8110 Cov.: 33

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.318

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.324 AC: 49186 AN: 151972 Hom.: 8126 Cov.: 33 AF XY: 0.327 AC XY: 24282 AN XY: 74232

African (AFR) AF: 0.280 AC: 11585 AN: 41416

American (AMR) AF: 0.315 AC: 4816 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1093 AN: 3472

East Asian (EAS) AF: 0.384 AC: 1985 AN: 5172

South Asian (SAS) AF: 0.371 AC: 1786 AN: 4812

European-Finnish (FIN) AF: 0.412 AC: 4339 AN: 10532

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.331 AC: 22500 AN: 67974

Other (OTH) AF: 0.323 AC: 682 AN: 2110

Alfa AF: 0.325 Hom.: 4160

Bravo AF: 0.315

Asia WGS AF: 0.402 AC: 1397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.2
DANN	Benign	0.69
PhyloP100		0.32
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1881691; hg19: chr7-154861393;