10-99445385-A-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000641293.1(GOT1-DT):​n.289-6400A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.818 in 152,178 control chromosomes in the GnomAD database, including 51,054 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 0.82 (51054 hom., 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.842 is higher than 0.05.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GOT1-DT	NR_183991.1		n.726-6400A>G		intron	N/A
	GOT1-DT	NR_183992.1		n.3006-6400A>G		intron	N/A
	GOT1-DT	NR_183993.1		n.618-6400A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GOT1-DT	ENST00000641293.1		n.289-6400A>G		intron	N/A
	GOT1-DT	ENST00000662162.1		n.732-6400A>G		intron	N/A
	GOT1-DT	ENST00000669986.1		n.2804-6400A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.817 AC: 124306 AN: 152060 Hom.: 51010 Cov.: 32

Gnomad AFR AF: 0.793

Gnomad AMI AF: 0.900

Gnomad AMR AF: 0.839

Gnomad ASJ AF: 0.831

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.712

Gnomad FIN AF: 0.800

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.848

Gnomad OTH AF: 0.827

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

GnomAD4 genome AF: 0.818 AC: 124409 AN: 152178 Hom.: 51054 Cov.: 32 AF XY: 0.812 AC XY: 60449 AN XY: 74406

African (AFR) AF: 0.793 AC: 32927 AN: 41524

American (AMR) AF: 0.839 AC: 12828 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.831 AC: 2886 AN: 3472

East Asian (EAS) AF: 0.659 AC: 3402 AN: 5160

South Asian (SAS) AF: 0.713 AC: 3433 AN: 4818

European-Finnish (FIN) AF: 0.800 AC: 8471 AN: 10592

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.848 AC: 57662 AN: 68002

Other (OTH) AF: 0.825 AC: 1744 AN: 2114

Alfa AF: 0.840 Hom.: 79814

Bravo AF: 0.822

Asia WGS AF: 0.686 AC: 2388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.7
DANN	Benign	0.75
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;