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. The variant received -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
• Publications: 6 publications found

Genes affected

ENSG00000272692 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000609200.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC101929234	NR_110304.1		n.975G>C		non_coding_transcript_exon	Exon 3 of 3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000272692	ENST00000609200.2	TSL:1	n.990G>C		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000272692	ENST00000814670.1		n.337+743G>C		intron	N/A

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

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.125 AC: 1 AN: 8

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.239 AC: 11 AN: 46

Other (OTH) AF: 0.500 AC: 1 AN: 2

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

African (AFR) AF: 0.129 AC: 5361 AN: 41514

American (AMR) AF: 0.111 AC: 1703 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 404 AN: 3470

East Asian (EAS) AF: 0.187 AC: 965 AN: 5174

South Asian (SAS) AF: 0.179 AC: 863 AN: 4818

European-Finnish (FIN) AF: 0.101 AC: 1074 AN: 10592

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9410 AN: 68012

Other (OTH) AF: 0.126 AC: 266 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.7
DANN	Benign	0.70
PhyloP100		2.9

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12782308;

hg19: chr10-77170685;