Genetic Variant TAT:c.*1276dupT (chr16-71566867-T-TA) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1BS2

The NM_000353.3(TAT):c.*1276dupT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0115 in 134,410 control chromosomes in the GnomAD database, including 7 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.012 ( 7 hom., cov: 32)

Failed GnomAD Quality Control

Consequence

TAT
NM_000353.3 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.565

Publications

0 publications found

Variant links:

Genes affected

TAT (HGNC:11573): (tyrosine aminotransferase) This nuclear gene encodes a mitochondrial protein tyrosine aminotransferase which is present in the liver and catalyzes the conversion of L-tyrosine into p-hydroxyphenylpyruvate. Mutations in this gene cause tyrosinemia (type II, Richner-Hanhart syndrome), a disorder accompanied by major skin and corneal lesions, with possible cognitive disability. A regulator gene for tyrosine aminotransferase is X-linked. [provided by RefSeq, Jul 2008]

TAT links:

TAT-AS1 (HGNC:51369): (TAT antisense RNA 1)

TAT-AS1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BS1

Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0115 (1549/134410) while in subpopulation AFR AF = 0.0161 (589/36622). AF 95% confidence interval is 0.015. There are 7 homozygotes in GnomAd4. There are 717 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 7 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000353.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TAT	NM_000353.3	MANE Select	c.*1276dupT	3_prime_UTR	Exon 12 of 12	NP_000344.1	P17735
TAT-AS1	NR_103851.1		n.284+679dupA	intron	N/A
TAT-AS1	NR_103852.1		n.258+679dupA	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TAT	ENST00000355962.5	TSL:1 MANE Select	c.*1276dupT	3_prime_UTR	Exon 12 of 12	ENSP00000348234.4	P17735
TAT	ENST00000895695.1		c.*1276dupT	3_prime_UTR	Exon 12 of 12	ENSP00000565754.1
TAT	ENST00000895697.1		c.*1276dupT	3_prime_UTR	Exon 11 of 11	ENSP00000565756.1

Frequencies

GnomAD3 genomes

AF:

0.0114

AC:

1538

AN:

134390

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0158

Gnomad AMI

AF:

0.0338

Gnomad AMR

AF:

0.0102

Gnomad ASJ

AF:

0.000943

Gnomad EAS

AF:

0.000851

Gnomad SAS

AF:

0.00139

Gnomad FIN

AF:

0.00547

Gnomad MID

AF:

0.00360

Gnomad NFE

AF:

0.0116

Gnomad OTH

AF:

0.0140

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AC:

AN:

Hom.:

Cov.:

AC XY:

AN XY:

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.0115

AC:

1549

AN:

134410

Hom.:

Cov.:

AF XY:

0.0111

AC XY:

717

AN XY:

64638

show subpopulations

African (AFR)

AF:

0.0161

AC:

589

AN:

36622

American (AMR)

AF:

0.0102

AC:

137

AN:

13496

Ashkenazi Jewish (ASJ)

AF:

0.000943

AC:

AN:

3182

East Asian (EAS)

AF:

0.000854

AC:

AN:

4682

South Asian (SAS)

AF:

0.00140

AC:

AN:

4290

European-Finnish (FIN)

AF:

0.00547

AC:

AN:

7492

Middle Eastern (MID)

AF:

0.00394

AC:

AN:

254

European-Non Finnish (NFE)

AF:

0.0116

AC:

716

AN:

61794

Other (OTH)

AF:

0.0139

AC:

AN:

1798

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.481

Heterozygous variant carriers

146

219

292

365

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00218

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.56

Mutation Taster

=100/0

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

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16-71566867-TAAAAAAAAA-TAAAAAAAAAA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over