Genetic Variant GOT1-DT:n.289-6400A>C (chr10-99445385-A-C) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000641293.1(GOT1-DT):n.289-6400A>C variant causes a intron 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)

Consequence

GOT1-DT
ENST00000641293.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0940

Publications

2 publications found

Variant links:

Genes affected

GOT1-DT (HGNC:55848): (GOT1 divergent transcript)

GOT1-DT links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000641293.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
GOT1-DT	NR_183991.1	n.726-6400A>C	intron	N/A
GOT1-DT	NR_183992.1	n.3006-6400A>C	intron	N/A
GOT1-DT	NR_183993.1	n.618-6400A>C	intron	N/A

Ensembl Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
GOT1-DT	ENST00000641293.1	n.289-6400A>C	intron	N/A
GOT1-DT	ENST00000662162.1	n.732-6400A>C	intron	N/A
GOT1-DT	ENST00000669986.1	n.2804-6400A>C	intron	N/A

Frequencies

GnomAD3 genomes

Cov.:

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

3.5

(source)

DANN

Benign

0.72

PhyloP100

-0.094

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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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