rs374725274

Variant names:

• chr15-67357415-A-C
• NM_001031715.3:c.708A>C

Your query was ambiguous. Multiple possible variants found:

• chr15-67357415-A-C
• chr15-67357415-A-G
• chr15-67357415-A-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001031715.3(IQCH):​c.708A>C​(p.Arg236Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: IQCH NM_001031715.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.222

Genes affected

IQCH (HGNC:25721): (IQ motif containing H)

IQCH-AS1 (HGNC:44104): (IQCH antisense RNA 1)

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.028639823).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IQCH	NM_001031715.3	c.708A>C	p.Arg236Ser	missense_variant	Exon 7 of 21	ENST00000335894.9	NP_001026885.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IQCH	ENST00000335894.9	c.708A>C	p.Arg236Ser	missense_variant	Exon 7 of 21	1	NM_001031715.3	ENSP00000336861.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 26

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.22
BayesDel_addAF	Benign	-0.32	T
BayesDel_noAF	Benign	-0.70
CADD	Benign	0.31
DANN	Benign	0.20
DEOGEN2	Benign	0.0067	T;.
Eigen	Benign	-1.7
Eigen_PC	Benign	-1.7
FATHMM_MKL	Benign	0.028	N
LIST_S2	Benign	0.39	T;T
M_CAP	Benign	0.0051	T
MetaRNN	Benign	0.029	T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	1.8	L;.
PrimateAI	Benign	0.28	T
PROVEAN	Benign	0.89	N;.
REVEL	Benign	0.017
Sift	Benign	0.77	T;.
Sift4G	Benign	0.77	T;T
Polyphen		0.0	B;B
Vest4		0.083
MutPred		0.21		Gain of phosphorylation at R236 (P = 0.007);.;
MVP		0.014
MPC		0.11
ClinPred		0.043	T
GERP RS		-1.8
Varity_R		0.073
gMVP		0.42

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: chr15-67649753;