Genetic Variant GATAD1:p.Gly59del (chr7-92447892-AGCG-A) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP3BP6

The NM_021167.5(GATAD1):c.175_177delGGC(p.Gly59del) variant causes a conservative inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000431 in 1,114,314 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in Lovd as Likely benign (no stars).

Frequency

Genomes: not found (cov: 33)

Exomes 𝑓: 0.000043 ( 0 hom. )

Consequence

GATAD1
NM_021167.5 conservative_inframe_deletion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.08

Variant links:

Genes affected

GATAD1 (HGNC:29941): (GATA zinc finger domain containing 1) The protein encoded by this gene contains a zinc finger at the N-terminus, and is thought to bind to a histone modification site that regulates gene expression. Mutations in this gene have been associated with autosomal recessive dilated cardiomyopathy. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jun 2012]

GATAD1 links:

TMBIM7P (HGNC:49212): (transmembrane BAX inhibitor motif containing 7, pseudogene)

TMBIM7P links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP3

Nonframeshift variant in repetitive region in NM_021167.5

BP6

Variant 7-92447892-AGCG-A is Benign according to our data. Variant chr7-92447892-AGCG-A is described in Lovd as [Likely_benign].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GATAD1	NM_021167.5 link	c.175_177delGGC	p.Gly59del	conservative_inframe_deletion	Exon 1 of 5	ENST00000287957.5	NP_066990.3	Q8WUU5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
GATAD1	ENST00000287957.5 link	c.175_177delGGC	p.Gly59del	conservative_inframe_deletion	Exon 1 of 5	1	NM_021167.5	ENSP00000287957.3	Q8WUU5
GATAD1	ENST00000644160.1 link	n.31_33delGGC		non_coding_transcript_exon_variant	Exon 1 of 2
GATAD1	ENST00000645746.1 link	n.175_177delGGC		non_coding_transcript_exon_variant	Exon 1 of 6			ENSP00000493785.1	A0A2R8Y4H1
TMBIM7P	ENST00000641474.1 link	n.-82_-80delCGC		upstream_gene_variant

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.000165

AC:

AN:

6072

Hom.:

AF XY:

0.00

AC XY:

AN XY:

2940

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.000185

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000431

AC:

AN:

1114314

Hom.:

AF XY:

0.0000563

AC XY:

AN XY:

532462

show subpopulations

Gnomad4 AFR exome

AF:

0.0000440

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.000141

Gnomad4 EAS exome

AF:

0.0000383

Gnomad4 SAS exome

AF:

0.000239

Gnomad4 FIN exome

AF:

0.000126

Gnomad4 NFE exome

AF:

0.0000331

Gnomad4 OTH exome

AF:

0.0000449

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

LitVar

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

7-92447892-AGCGGCGGCGGCG-AGCGGCGGCG

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