Genetic Variant ST7:p.Leu38Gln (chr7-116953653-T-A) – ACMG Classification: Uncertain_significance (2 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001369598.1(ST7):c.113T>A(p.Leu38Gln) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L38P) has been classified 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: 4.23

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 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

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.113T>A	p.Leu38Gln	missense	Exon 1 of 16	NP_001356527.1	H7BXS2
ST7	NM_021908.3		c.113T>A	p.Leu38Gln	missense	Exon 1 of 16	NP_068708.1	X5DRA0
ST7	NM_001369601.1		c.113T>A	p.Leu38Gln	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.113T>A	p.Leu38Gln	missense	Exon 1 of 16	ENSP00000325673.3	H7BXS2
ST7	ENST00000265437.9	TSL:1	c.113T>A	p.Leu38Gln	missense	Exon 1 of 16	ENSP00000265437.5	Q9NRC1-1
ST7	ENST00000393451.7	TSL:1	c.113T>A	p.Leu38Gln	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:

1350968

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

672852

African (AFR)

AF:

0.00

AC:

AN:

27670

American (AMR)

AF:

0.00

AC:

AN:

38160

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

21992

East Asian (EAS)

AF:

0.00

AC:

AN:

30516

South Asian (SAS)

AF:

0.00

AC:

AN:

80558

European-Finnish (FIN)

AF:

0.00

AC:

AN:

49156

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5270

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1044454

Other (OTH)

AF:

0.00

AC:

AN:

53192

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

Pathogenic

0.92

BayesDel_addAF

Uncertain

0.012

BayesDel_noAF

Benign

-0.22

CADD

Uncertain

(source)

DANN

Uncertain

0.99

DEOGEN2

Benign

0.042

Eigen

Benign

0.075

Eigen_PC

Benign

-0.022

FATHMM_MKL

Uncertain

0.79

LIST_S2

Uncertain

0.97

M_CAP

Uncertain

0.12

MetaRNN

Uncertain

0.54

MetaSVM

Benign

-0.85

MutationAssessor

Uncertain

2.2

PhyloP100

4.2

PrimateAI

Uncertain

0.72

PROVEAN

Benign

-1.9

REVEL

Benign

0.27

Sift

Uncertain

0.0010

Sift4G

Uncertain

0.0040

Polyphen

1.0

Vest4

0.73

MutPred

0.73

Loss of stability (P = 0.0213)

MVP

0.10

MPC

0.53

ClinPred

0.92

GERP RS

2.3

PromoterAI

0.013

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.50

gMVP

0.88

Mutation Taster

=76/24

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