rs605367

chr1-23192031-T-Cchr1-23192031-T-G

Variant summary

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

The NM_000864.5(HTR1D):c.*1055A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 142,496 control chromosomes in the GnomAD database, including 11,511 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 0.40 (11511 hom., cov: 24)
  • Failed GnomAD Quality Control
• Consequence: HTR1D NM_000864.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950

Genes affected

HTR1D (HGNC:5289): (5-hydroxytryptamine receptor 1D) Enables G protein-coupled serotonin receptor activity. Involved in adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway and intestine smooth muscle contraction. Is integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.509 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HTR1D	NM_000864.5	c.*1055A>G		3_prime_UTR_variant	2/2	ENST00000374619.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HTR1D	ENST00000374619.2	c.*1055A>G		3_prime_UTR_variant	2/2		NM_000864.5	P1

Frequencies

GnomAD3 genomes AF: 0.400 AC: 56998 AN: 142348 Hom.: 11478 Cov.: 24

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.438

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.395

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.401 AC: 57098 AN: 142496 Hom.: 11511 Cov.: 24 AF XY: 0.398 AC XY: 27538 AN XY: 69220

Gnomad4 AFR AF: 0.515

Gnomad4 AMR AF: 0.331

Gnomad4 ASJ AF: 0.416

Gnomad4 EAS AF: 0.307

Gnomad4 SAS AF: 0.320

Gnomad4 FIN AF: 0.381

Gnomad4 NFE AF: 0.361

Gnomad4 OTH AF: 0.395

Alfa AF: 0.355 Hom.: 2309

Bravo AF: 0.389

Asia WGS AF: 0.286 AC: 994 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.8
Dann	Benign	0.59

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs605367; hg19: chr1-23518524;