chr10-90853660-T-C

Variant names:

• chr10-90853660-T-C
• rs12761105
• NM_019859.4:c.539+3473A>G

Variant summary

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

The NM_019859.4(HTR7):​c.539+3473A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 151,940 control chromosomes in the GnomAD database, including 4,061 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 0.21 (4061 hom., cov: 31)
• Consequence: HTR7 NM_019859.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.478
• Publications: 3 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.349 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HTR7	NM_019859.4	MANE Select	c.539+3473A>G		intron	N/A	NP_062873.1	P34969-1
	HTR7	NM_000872.5		c.539+3473A>G		intron	N/A	NP_000863.1	P34969-2
	HTR7	NM_019860.4		c.539+3473A>G		intron	N/A	NP_062874.1	P34969-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HTR7	ENST00000336152.8	TSL:1 MANE Select	c.539+3473A>G		intron	N/A	ENSP00000337949.3	P34969-1
	HTR7	ENST00000277874.10	TSL:1	c.539+3473A>G		intron	N/A	ENSP00000277874.6	P34969-2
	HTR7	ENST00000371719.2	TSL:1	c.539+3473A>G		intron	N/A	ENSP00000360784.2	P34969-3

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31338 AN: 151822 Hom.: 4053 Cov.: 31

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.228

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.206 AC: 31370 AN: 151940 Hom.: 4061 Cov.: 31 AF XY: 0.208 AC XY: 15436 AN XY: 74256

African (AFR) AF: 0.354 AC: 14659 AN: 41382

American (AMR) AF: 0.225 AC: 3432 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 553 AN: 3472

East Asian (EAS) AF: 0.274 AC: 1416 AN: 5168

South Asian (SAS) AF: 0.232 AC: 1114 AN: 4808

European-Finnish (FIN) AF: 0.121 AC: 1277 AN: 10568

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.122 AC: 8304 AN: 67966

Other (OTH) AF: 0.226 AC: 475 AN: 2102

Alfa AF: 0.174 Hom.: 397

Bravo AF: 0.224

Asia WGS AF: 0.235 AC: 816 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.7
DANN	Benign	0.83
PhyloP100		0.48
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: rs12761105; hg19: chr10-92613417;