rs10492243

chr12-30830616-T-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, non coding transcript 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: ENST00000648700.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.32

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000648700.1	n.246+30595T>C		intron_variant, non_coding_transcript_variant

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;