chr10-99445385-A-C

Variant names:

• chr10-99445385-A-C
• rs2490286
• ENST00000641293.1:n.289-6400A>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0940
• Publications: 2 publications found

Genes affected

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

ACMG classification

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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GOT1-DT	NR_183991.1	n.726-6400A>C		intron_variant	Intron 2 of 3
GOT1-DT	NR_183992.1	n.3006-6400A>C		intron_variant	Intron 1 of 2
GOT1-DT	NR_183993.1	n.618-6400A>C		intron_variant	Intron 3 of 4
GOT1-DT	NR_183994.1	n.745-6400A>C		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GOT1-DT	ENST00000641293.1	n.289-6400A>C		intron_variant	Intron 2 of 3
GOT1-DT	ENST00000662162.1	n.732-6400A>C		intron_variant	Intron 2 of 3
GOT1-DT	ENST00000669986.1	n.2804-6400A>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.5
DANN	Benign	0.72
PhyloP100		-0.094

Splicing

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

Other links and lift over

dbSNP: rs2490286; hg19: chr10-101205142;