rs10492243

Variant names:

• chr12-30830616-T-C
• rs10492243
• ENST00000648700.1:n.246+30595T>C

Variant summary

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

The ENST00000648700.1(ENSG00000285517):​n.246+30595T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 151,970 control chromosomes in the GnomAD database, including 2,667 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 0.16 (2667 hom., cov: 32)
• Consequence: ENSG00000285517 ENST00000648700.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.32

Genes affected

ENSG00000285517 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285517	ENST00000648700.1	n.246+30595T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24592 AN: 151852 Hom.: 2662 Cov.: 32

Gnomad AFR AF: 0.0646

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.162 AC: 24601 AN: 151970 Hom.: 2667 Cov.: 32 AF XY: 0.166 AC XY: 12361 AN XY: 74284

Gnomad4 AFR AF: 0.0644

Gnomad4 AMR AF: 0.366

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.140

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.184

Alfa AF: 0.184 Hom.: 3617

Bravo AF: 0.174

Asia WGS AF: 0.179 AC: 621 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.8
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10492243; hg19: chr12-30983550;