chr10-90749433-C-T

Position:

• chr10-90749433-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_019859.4(HTR7):​c.701G>A​(p.Ser234Asn) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: HTR7 NM_019859.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 6.16

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

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HTR7	NM_019859.4	c.701G>A	p.Ser234Asn	missense_variant	2/4	ENST00000336152.8	NP_062873.1
HTR7	NM_000872.5	c.701G>A	p.Ser234Asn	missense_variant	2/3		NP_000863.1
HTR7	NM_019860.4	c.701G>A	p.Ser234Asn	missense_variant	2/3		NP_062874.1
HTR7	XM_024447973.2	c.107G>A	p.Ser36Asn	missense_variant	2/4		XP_024303741.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HTR7	ENST00000336152.8	c.701G>A	p.Ser234Asn	missense_variant	2/4	1	NM_019859.4	ENSP00000337949
HTR7	ENST00000277874.10	c.701G>A	p.Ser234Asn	missense_variant	2/3	1		ENSP00000277874	A1
HTR7	ENST00000371719.2	c.701G>A	p.Ser234Asn	missense_variant	2/3	1		ENSP00000360784	P4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Apr 13, 2023

The c.701G>A (p.S234N) alteration is located in exon 2 (coding exon 2) of the HTR7 gene. This alteration results from a G to A substitution at nucleotide position 701, causing the serine (S) at amino acid position 234 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.97
BayesDel_addAF	Benign	-0.096	T
BayesDel_noAF	Benign	-0.38
CADD	Pathogenic	27
DANN	Uncertain	1.0
DEOGEN2	Benign	0.22	T;.;.
Eigen	Uncertain	0.58
Eigen_PC	Uncertain	0.63
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.94	D;D;D
M_CAP	Benign	0.016	T
MetaRNN	Uncertain	0.70	D;D;D
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.4	L;L;L
MutationTaster	Benign	1.0	D;D;D;D
PrimateAI	Pathogenic	0.86	D
PROVEAN	Benign	-2.3	N;N;N
REVEL	Benign	0.15
Sift	Benign	0.15	T;T;T
Sift4G	Benign	0.25	T;T;T
Polyphen		0.97	D;D;.
Vest4		0.64
MutPred		0.58		Loss of ubiquitination at K229 (P = 0.0853);Loss of ubiquitination at K229 (P = 0.0853);Loss of ubiquitination at K229 (P = 0.0853);
MVP		0.76
MPC		1.1
ClinPred		0.96	D
GERP RS		5.3
Varity_R		0.58
gMVP		0.86

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr10-92509190;