Variant 17-29574957-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000225394.8(GIT1):c.2074-43T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.742 in 1,502,650 control chromosomes in the GnomAD database, including 415,737 homozygotes. 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: 𝑓 0.76 ( 43822 hom., cov: 31)

Exomes 𝑓: 0.74 ( 371915 hom. )

Consequence

GIT1
ENST00000225394.8 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.512

Variant links:

Genes affected

GIT1 (HGNC:4272): (GIT ArfGAP 1) Enables gamma-tubulin binding activity. Involved in positive regulation of microtubule nucleation and regulation of cytokinesis. Located in several cellular components, including focal adhesion; microtubule cytoskeleton; and mitochondrion. Implicated in attention deficit hyperactivity disorder. Biomarker of Huntington's disease. [provided by Alliance of Genome Resources, Apr 2022]

GIT1 links:

ABHD15-AS1 (HGNC:49685): (ABHD15 antisense RNA 1)

ABHD15-AS1 links:

TP53I13 (HGNC:):

TP53I13 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=9.3827845E-7).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.9 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GIT1	NM_014030.4 linkuse as main transcript	c.2074-43T>C		intron_variant		ENST00000225394.8	NP_054749.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GIT1	ENST00000225394.8 linkuse as main transcript	c.2074-43T>C		intron_variant		1	NM_014030.4	ENSP00000225394	A1	Q9Y2X7-1
ABHD15-AS1	ENST00000581474.1 linkuse as main transcript	n.153+14258A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes

AF:

0.757

AC:

114922

AN:

151868

Hom.:

43774

Cov.:

show subpopulations

Gnomad AFR

AF:

0.814

Gnomad AMI

AF:

0.632

Gnomad AMR

AF:

0.738

Gnomad ASJ

AF:

0.794

Gnomad EAS

AF:

0.922

Gnomad SAS

AF:

0.720

Gnomad FIN

AF:

0.667

Gnomad MID

AF:

0.741

Gnomad NFE

AF:

0.730

Gnomad OTH

AF:

0.757

GnomAD3 exomes

AF:

0.745

AC:

128282

AN:

172080

Hom.:

48087

AF XY:

0.743

AC XY:

68759

AN XY:

92576

show subpopulations

Gnomad AFR exome

AF:

0.812

Gnomad AMR exome

AF:

0.723

Gnomad ASJ exome

AF:

0.795

Gnomad EAS exome

AF:

0.919

Gnomad SAS exome

AF:

0.724

Gnomad FIN exome

AF:

0.673

Gnomad NFE exome

AF:

0.729

Gnomad OTH exome

AF:

0.745

GnomAD4 exome

AF:

0.741

AC:

1000666

AN:

1350664

Hom.:

371915

Cov.:

AF XY:

0.739

AC XY:

491907

AN XY:

665250

show subpopulations

Gnomad4 AFR exome

AF:

0.815

Gnomad4 AMR exome

AF:

0.725

Gnomad4 ASJ exome

AF:

0.789

Gnomad4 EAS exome

AF:

0.917

Gnomad4 SAS exome

AF:

0.723

Gnomad4 FIN exome

AF:

0.671

Gnomad4 NFE exome

AF:

0.736

Gnomad4 OTH exome

AF:

0.744

GnomAD4 genome

AF:

0.757

AC:

115019

AN:

151986

Hom.:

43822

Cov.:

AF XY:

0.755

AC XY:

56109

AN XY:

74272

show subpopulations

Gnomad4 AFR

AF:

0.814

Gnomad4 AMR

AF:

0.738

Gnomad4 ASJ

AF:

0.794

Gnomad4 EAS

AF:

0.922

Gnomad4 SAS

AF:

0.720

Gnomad4 FIN

AF:

0.667

Gnomad4 NFE

AF:

0.730

Gnomad4 OTH

AF:

0.757

Alfa

AF:

0.737

Hom.:

22557

Bravo

AF:

0.766

TwinsUK

AF:

0.736

AC:

2729

ALSPAC

AF:

0.751

AC:

2894

ESP6500AA

AF:

0.809

AC:

3535

ESP6500EA

AF:

0.740

AC:

6321

ExAC

AF:

0.705

AC:

81475

Asia WGS

AF:

0.815

AC:

2836

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.72

BayesDel_noAF

Benign

-0.66

CADD

Benign

0.065

DANN

Benign

0.27

FATHMM_MKL

Benign

0.037

LIST_S2

Benign

0.19

MetaRNN

Benign

9.4e-7

MutationTaster

Benign

1.0

P;P;P;P

Vest4

0.040

GERP RS

-7.4

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over