rs17526697

Variant names:

• chr10-90740762-G-A
• rs17526697
• NM_019859.4:c.*1720C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_019859.4(HTR7):​c.*1720C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0657 in 152,382 control chromosomes in the GnomAD database, including 416 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 0.066 (416 hom., cov: 32)
  • Exomes 𝑓: 0.077 (0 hom.)
• Consequence: HTR7 NM_019859.4 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207
• Publications: 6 publications found

Genes affected

HTR7 (HGNC:5302): (5-hydroxytryptamine receptor 7) The neurotransmitter, serotonin, is thought to play a role in various cognitive and behavioral functions. The serotonin receptor encoded by this gene belongs to the superfamily of G protein-coupled receptors and the gene is a candidate locus for involvement in autistic disorder and other neuropsychiatric disorders. Three splice variants have been identified which encode proteins that differ in the length of their carboxy terminal ends. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0967 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_019859.4. 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
	HTR7	NM_019859.4	MANE Select	c.*1720C>T		downstream_gene	N/A	NP_062873.1
	HTR7	NM_000872.5		c.*1724C>T		downstream_gene	N/A	NP_000863.1
	HTR7	NM_019860.4		c.*1768C>T		downstream_gene	N/A	NP_062874.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HTR7	ENST00000336152.8	TSL:1 MANE Select	c.*1720C>T		downstream_gene	N/A	ENSP00000337949.3
	HTR7	ENST00000277874.10	TSL:1	c.*1724C>T		downstream_gene	N/A	ENSP00000277874.6
	HTR7	ENST00000371719.2	TSL:1	c.*1768C>T		downstream_gene	N/A	ENSP00000360784.2

Frequencies

GnomAD3 genomes AF: 0.0658 AC: 10002 AN: 152068 Hom.: 417 Cov.: 32

Gnomad AFR AF: 0.0175

Gnomad AMI AF: 0.0549

Gnomad AMR AF: 0.0642

Gnomad ASJ AF: 0.0732

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0816

Gnomad FIN AF: 0.0652

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0987

Gnomad OTH AF: 0.0755

GnomAD4 exome AF: 0.0765 AC: 15 AN: 196 Hom.: 0 AF XY: 0.0672 AC XY: 9 AN XY: 134

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) AF: 0.0773 AC: 15 AN: 194

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.0657 AC: 9994 AN: 152186 Hom.: 416 Cov.: 32 AF XY: 0.0640 AC XY: 4762 AN XY: 74406

African (AFR) AF: 0.0174 AC: 722 AN: 41546

American (AMR) AF: 0.0641 AC: 979 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0732 AC: 254 AN: 3472

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5182

South Asian (SAS) AF: 0.0821 AC: 396 AN: 4826

European-Finnish (FIN) AF: 0.0652 AC: 690 AN: 10584

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0987 AC: 6710 AN: 67984

Other (OTH) AF: 0.0743 AC: 157 AN: 2114

Alfa AF: 0.0912 Hom.: 1236

Bravo AF: 0.0631

Asia WGS AF: 0.0300 AC: 108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.80
DANN	Benign	0.50
PhyloP100		0.21
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs17526697; hg19: chr10-92500519;