rs1881691

chr7-155069683-A-Cchr7-155069683-A-T

Variant summary

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

The NR_038945.1(HTR5A-AS1):n.525-438T>G variant causes a intron, non coding transcript 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 NR_038945.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.321

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=-0.84).
• 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/exons	MANE	UniProt
HTR5A-AS1	NR_038945.1	n.525-438T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HTR5A-AS1	ENST00000395731.5	n.525-438T>G		intron_variant, non_coding_transcript_variant		1
HTR5A-AS1	ENST00000671665.1	n.1418-438T>G		intron_variant, non_coding_transcript_variant
HTR5A-AS1	ENST00000493904.3	n.552-438T>G		intron_variant, non_coding_transcript_variant		4
HTR5A-AS1	ENST00000655797.1	n.850-438T>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.315

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.384

Gnomad4 SAS AF: 0.371

Gnomad4 FIN AF: 0.412

Gnomad4 NFE AF: 0.331

Gnomad4 OTH AF: 0.323

Alfa AF: 0.325 Hom.: 3556

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1881691; hg19: chr7-154861393;