chr1-23192031-T-C

Variant names:

• chr1-23192031-T-C
• rs605367
• NM_000864.5:c.*1055A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000864.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HTR1D	NM_000864.5	MANE Select	c.*1055A>G		3_prime_UTR	Exon 2 of 2	NP_000855.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HTR1D	ENST00000374619.2	TSL:6 MANE Select	c.*1055A>G		3_prime_UTR	Exon 2 of 2	ENSP00000363748.1

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

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

African (AFR) AF: 0.515 AC: 20289 AN: 39432

American (AMR) AF: 0.331 AC: 4731 AN: 14298

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1382 AN: 3320

East Asian (EAS) AF: 0.307 AC: 1343 AN: 4370

South Asian (SAS) AF: 0.320 AC: 1254 AN: 3922

European-Finnish (FIN) AF: 0.381 AC: 3587 AN: 9414

Middle Eastern (MID) AF: 0.451 AC: 128 AN: 284

European-Non Finnish (NFE) AF: 0.361 AC: 23320 AN: 64586

Other (OTH) AF: 0.395 AC: 797 AN: 2016

Alfa AF: 0.366 Hom.: 2836

Bravo AF: 0.389

Asia WGS AF: 0.286 AC: 994 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.8
DANN	Benign	0.59
PhyloP100		-0.095
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs605367; hg19: chr1-23518524;