10-90800151-G-T

Variant names:

• chr10-90800151-G-T
• rs7916403
• NM_019859.4:c.540-50557C>A

Variant summary

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

The NM_019859.4(HTR7):​c.540-50557C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 152,026 control chromosomes in the GnomAD database, including 20,166 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 0.51 (20166 hom., cov: 32)
• Consequence: HTR7 NM_019859.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75
• Publications: 14 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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HTR7	NM_019859.4	c.540-50557C>A		intron_variant	Intron 1 of 3	ENST00000336152.8	NP_062873.1
HTR7	NM_000872.5	c.540-50557C>A		intron_variant	Intron 1 of 2		NP_000863.1
HTR7	NM_019860.4	c.540-50557C>A		intron_variant	Intron 1 of 2		NP_062874.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HTR7	ENST00000336152.8	c.540-50557C>A		intron_variant	Intron 1 of 3	1	NM_019859.4	ENSP00000337949.3
HTR7	ENST00000277874.10	c.540-50557C>A		intron_variant	Intron 1 of 2	1		ENSP00000277874.6
HTR7	ENST00000371719.2	c.540-50557C>A		intron_variant	Intron 1 of 2	1		ENSP00000360784.2

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76839 AN: 151908 Hom.: 20133 Cov.: 32

Gnomad AFR AF: 0.665

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.506 AC: 76933 AN: 152026 Hom.: 20166 Cov.: 32 AF XY: 0.505 AC XY: 37541 AN XY: 74330

African (AFR) AF: 0.665 AC: 27583 AN: 41476

American (AMR) AF: 0.456 AC: 6973 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.483 AC: 1678 AN: 3472

East Asian (EAS) AF: 0.480 AC: 2471 AN: 5144

South Asian (SAS) AF: 0.483 AC: 2331 AN: 4824

European-Finnish (FIN) AF: 0.424 AC: 4476 AN: 10558

Middle Eastern (MID) AF: 0.462 AC: 135 AN: 292

European-Non Finnish (NFE) AF: 0.439 AC: 29829 AN: 67944

Other (OTH) AF: 0.483 AC: 1022 AN: 2116

Alfa AF: 0.459 Hom.: 45452

Bravo AF: 0.515

Asia WGS AF: 0.490 AC: 1700 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.18
DANN	Benign	0.15
PhyloP100		-1.8
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: rs7916403; hg19: chr10-92559908;