rs12782308

Variant names:

• chr10-75410927-G-C
• rs12782308
• ENST00000609200.2:n.990G>C

Your query was ambiguous. Multiple possible variants found:

• chr10-75410927-G-C
• chr10-75410927-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000609200.2(ENSG00000272692):​n.990G>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 0.133 in 152,248 control chromosomes in the GnomAD database, including 1,357 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 0.13 (1355 hom., cov: 32)
  • Exomes 𝑓: 0.22 (2 hom.)
• Consequence: ENSG00000272692 ENST00000609200.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.94

Genes affected

ENSG00000272692 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929234	NR_110304.1	n.975G>C		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000272692	ENST00000609200.2	n.990G>C		non_coding_transcript_exon_variant	Exon 3 of 3	1

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20188 AN: 152070 Hom.: 1352 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.121

GnomAD4 exome AF: 0.217 AC: 13 AN: 60 Hom.: 2 Cov.: 0 AF XY: 0.175 AC XY: 7 AN XY: 40

Gnomad4 AFR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.125

Gnomad4 NFE exome AF: 0.239

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.133 AC: 20202 AN: 152188 Hom.: 1355 Cov.: 32 AF XY: 0.130 AC XY: 9683 AN XY: 74396

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.179

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.126

Alfa AF: 0.0583 Hom.: 72

Bravo AF: 0.131

Asia WGS AF: 0.195 AC: 679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.7
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12782308; hg19: chr10-77170685;