7-150369830-G-T

Variant names:

• chr7-150369830-G-T
• NM_001099695.2:c.119G>T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001099695.2(REPIN1):​c.119G>T​(p.Ser40Ile) 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: REPIN1 NM_001099695.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.747

Genes affected

REPIN1 (HGNC:17922): (replication initiator 1) Enables RNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within positive regulation of glucose import and regulation of fatty acid transport. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ZNF775 (HGNC:28501): (zinc finger protein 775) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

REPIN1-AS1 (HGNC:41201): (REPIN1 antisense RNA 1)

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.15554234).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
REPIN1	NM_001099695.2	c.119G>T	p.Ser40Ile	missense_variant	Exon 2 of 3	ENST00000489432.7	NP_001093165.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
REPIN1	ENST00000489432.7	c.119G>T	p.Ser40Ile	missense_variant	Exon 2 of 3	2	NM_001099695.2	ENSP00000417291.2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 33

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Feb 09, 2025

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.119G>T (p.S40I) alteration is located in exon 2 (coding exon 1) of the REPIN1 gene. This alteration results from a G to T substitution at nucleotide position 119, causing the serine (S) at amino acid position 40 to be replaced by an isoleucine (I). 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
BayesDel_addAF	Benign	-0.15	T
BayesDel_noAF	Benign	-0.46
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Benign	0.017	.;.;T;.;T
Eigen	Benign	-0.12
Eigen_PC	Benign	-0.080
FATHMM_MKL	Benign	0.17	N
LIST_S2	Benign	0.74	.;T;T;T;T
M_CAP	Benign	0.013	T
MetaRNN	Benign	0.16	T;T;T;T;T
MetaSVM	Benign	-0.92	T
PrimateAI	Benign	0.44	T
PROVEAN	Pathogenic	-6.0	D;N;N;D;N
REVEL	Benign	0.055
Sift	Pathogenic	0.0	D;D;T;D;T
Sift4G	Pathogenic	0.0	D;T;D;D;T
Vest4		0.20
MutPred		0.28		Loss of phosphorylation at S40 (P = 0.0169);Loss of phosphorylation at S40 (P = 0.0169);.;Loss of phosphorylation at S40 (P = 0.0169);.;
MVP		0.10
MPC		1.3
ClinPred		0.94	D
GERP RS		4.0
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.7
gMVP		0.31

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: chr7-150066919;