dbSNP rs130058: LOC105377864:c.-10895T>A (chr6-77463564-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The XM_047419659.1(LOC105377864):c.-10895T>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 673,436 control chromosomes in the GnomAD database, including 26,820 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 0.23 ( 5071 hom., cov: 32)

Exomes 𝑓: 0.28 ( 21749 hom. )

Consequence

LOC105377864
XM_047419659.1 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.677

Variant links:

Genes affected

LOC105377864 (HGNC:):

LOC105377864 links:

HTR1B (HGNC:5287): (5-hydroxytryptamine receptor 1B) The protein encoded by this intronless gene is a G-protein coupled receptor for serotonin (5-hydroxytryptamine). Ligand binding activates second messengers that inhibit the activity of adenylate cyclase and manage the release of serotonin, dopamine, and acetylcholine in the brain. The encoded protein may be involved in several neuropsychiatric disorders and therefore is often a target of antidepressant and other psychotherapeutic drugs. [provided by RefSeq, Nov 2015]

HTR1B links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.54).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HTR1B	NM_000863.3 link	c.-161A>T		upstream_gene_variant		ENST00000369947.5	NP_000854.1	P28222X5D7I5A8K215

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HTR1B	ENST00000369947.5 link	c.-161A>T		upstream_gene_variant		6	NM_000863.3	ENSP00000358963.3		P28222

Frequencies

GnomAD3 genomes

AF:

0.232

AC:

35268

AN:

151876

Hom.:

5069

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0703

Gnomad AMI

AF:

0.359

Gnomad AMR

AF:

0.281

Gnomad ASJ

AF:

0.329

Gnomad EAS

AF:

0.0940

Gnomad SAS

AF:

0.252

Gnomad FIN

AF:

0.378

Gnomad MID

AF:

0.272

Gnomad NFE

AF:

0.298

Gnomad OTH

AF:

0.267

GnomAD4 exome

AF:

0.278

AC:

145206

AN:

521440

Hom.:

21749

Cov.:

AF XY:

0.278

AC XY:

75293

AN XY:

271252

show subpopulations

Gnomad4 AFR exome

AF:

0.0654

Gnomad4 AMR exome

AF:

0.296

Gnomad4 ASJ exome

AF:

0.328

Gnomad4 EAS exome

AF:

0.0732

Gnomad4 SAS exome

AF:

0.250

Gnomad4 FIN exome

AF:

0.361

Gnomad4 NFE exome

AF:

0.300

Gnomad4 OTH exome

AF:

0.279

GnomAD4 genome

AF:

0.232

AC:

35280

AN:

151996

Hom.:

5071

Cov.:

AF XY:

0.235

AC XY:

17495

AN XY:

74296

show subpopulations

Gnomad4 AFR

AF:

0.0702

Gnomad4 AMR

AF:

0.281

Gnomad4 ASJ

AF:

0.329

Gnomad4 EAS

AF:

0.0934

Gnomad4 SAS

AF:

0.253

Gnomad4 FIN

AF:

0.378

Gnomad4 NFE

AF:

0.298

Gnomad4 OTH

AF:

0.266

Alfa

AF:

0.143

Hom.:

280

Bravo

AF:

0.220

Asia WGS

AF:

0.176

AC:

612

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

DANN

Benign

0.83

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over