10-99432725-G-C

Variant names:

• chr10-99432725-G-C
• rs2490281
• ENST00000647895.2:n.1807G>C

Variant summary

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

The ENST00000647895.2(GOT1-DT):​n.1807G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0458 in 152,176 control chromosomes in the GnomAD database, including 213 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 0.046 (213 hom., cov: 32)
• Consequence: GOT1-DT ENST00000647895.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.256
• 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0774 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000647895.2. 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_183992.1		n.1790G>C		non_coding_transcript_exon	Exon 1 of 3
	GOT1-DT	NR_183995.1		n.1126G>C		non_coding_transcript_exon	Exon 2 of 3
	GOT1-DT	NR_183998.1		n.1126G>C		non_coding_transcript_exon	Exon 2 of 5

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GOT1-DT	ENST00000647895.2		n.1807G>C		non_coding_transcript_exon	Exon 1 of 2
	GOT1-DT	ENST00000652903.1		n.1093G>C		non_coding_transcript_exon	Exon 1 of 3
	GOT1-DT	ENST00000657109.1		n.1796G>C		non_coding_transcript_exon	Exon 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0458 AC: 6957 AN: 152058 Hom.: 212 Cov.: 32

Gnomad AFR AF: 0.0796

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0316

Gnomad ASJ AF: 0.0409

Gnomad EAS AF: 0.0727

Gnomad SAS AF: 0.0585

Gnomad FIN AF: 0.0259

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0293

Gnomad OTH AF: 0.0373

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

GnomAD4 genome AF: 0.0458 AC: 6963 AN: 152176 Hom.: 213 Cov.: 32 AF XY: 0.0458 AC XY: 3407 AN XY: 74404

African (AFR) AF: 0.0796 AC: 3305 AN: 41512

American (AMR) AF: 0.0315 AC: 482 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0409 AC: 142 AN: 3472

East Asian (EAS) AF: 0.0725 AC: 374 AN: 5160

South Asian (SAS) AF: 0.0584 AC: 281 AN: 4814

European-Finnish (FIN) AF: 0.0259 AC: 275 AN: 10598

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0293 AC: 1995 AN: 68006

Other (OTH) AF: 0.0379 AC: 80 AN: 2112

Alfa AF: 0.00775 Hom.: 0

Bravo AF: 0.0478

Asia WGS AF: 0.0810 AC: 284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.1
DANN	Benign	0.80
PhyloP100		0.26
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

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

Other links and lift over

dbSNP: rs2490281; hg19: chr10-101192482;