Genetic Variant NM_001369598.1:c.97T>C (chr7-116953637-T-C) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001369598.1(ST7):c.97T>C(p.Phe33Leu) 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. 14/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 31)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

ST7
NM_001369598.1 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.76

Publications

0 publications found

Variant links:

Genes affected

ST7 (HGNC:11351): (suppression of tumorigenicity 7) The gene for this product maps to a region on chromosome 7 identified as an autism-susceptibility locus. Mutation screening of the entire coding region in autistic individuals failed to identify phenotype-specific variants, suggesting that coding mutations for this gene are unlikely to be involved in the etiology of autism. The function of this gene product has not been determined. Transcript variants encoding different isoforms of this protein have been described. [provided by RefSeq, Jul 2008]

ST7 links:

ST7-AS1 (HGNC:16000): (ST7 antisense RNA 1)

ST7-AS1 links:

ST7-OT4 (HGNC:18835): (ST7 overlapping transcript 4)

ST7-OT4 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.10506487).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001369598.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
ST7	NM_001369598.1	MANE Select	c.97T>C	p.Phe33Leu	missense	Exon 1 of 16	NP_001356527.1	H7BXS2
ST7	NM_021908.3		c.97T>C	p.Phe33Leu	missense	Exon 1 of 16	NP_068708.1	X5DRA0
ST7	NM_001369601.1		c.97T>C	p.Phe33Leu	missense	Exon 1 of 16	NP_001356530.1	E7EPD9

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
ST7	ENST00000323984.8	TSL:5 MANE Select	c.97T>C	p.Phe33Leu	missense	Exon 1 of 16	ENSP00000325673.3	H7BXS2
ST7	ENST00000265437.9	TSL:1	c.97T>C	p.Phe33Leu	missense	Exon 1 of 16	ENSP00000265437.5	Q9NRC1-1
ST7	ENST00000393451.7	TSL:1	c.97T>C	p.Phe33Leu	missense	Exon 1 of 15	ENSP00000377097.3	Q9NRC1-2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1357770

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

676288

African (AFR)

AF:

0.00

AC:

AN:

27904

American (AMR)

AF:

0.00

AC:

AN:

38626

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

22248

East Asian (EAS)

AF:

0.00

AC:

AN:

31086

South Asian (SAS)

AF:

0.00

AC:

AN:

81278

European-Finnish (FIN)

AF:

0.00

AC:

AN:

49478

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5296

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1048264

Other (OTH)

AF:

0.00

AC:

AN:

53590

GnomAD4 genome

Cov.:

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.48

BayesDel_addAF

Benign

-0.20

BayesDel_noAF

Benign

-0.53

CADD

Benign

(source)

DANN

Benign

0.84

DEOGEN2

Benign

0.0085

Eigen

Benign

-0.65

Eigen_PC

Benign

-0.57

FATHMM_MKL

Benign

0.41

LIST_S2

Benign

0.79

M_CAP

Benign

0.018

MetaRNN

Benign

0.11

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.81

PhyloP100

2.8

PrimateAI

Pathogenic

0.81

PROVEAN

Benign

-0.020

REVEL

Benign

0.10

Sift

Benign

0.74

Sift4G

Benign

0.66

Polyphen

0.0

Vest4

0.38

MutPred

0.52

Loss of MoRF binding (P = 0.1311)

MVP

0.043

MPC

0.16

ClinPred

0.23

GERP RS

2.4

PromoterAI

0.0040

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.064

gMVP

0.65

Mutation Taster

=77/23

polymorphism

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over