rs10506318

Variant names:

• chr12-53794398-T-G
• rs10506318
• ENST00000652339.1:n.214-54461T>G

Variant summary

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

The ENST00000652339.1(ENSG00000286069):​n.214-54461T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,212 control chromosomes in the GnomAD database, including 2,504 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 0.10 (2504 hom., cov: 32)
• Consequence: ENSG00000286069 ENST00000652339.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.733
• Publications: 1 publications found

Genes affected

ENSG00000286069 (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 (AFR) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378250	NR_189097.1	n.295+54510T>G		intron_variant	Intron 1 of 2
LOC105378250	NR_189098.1	n.296-54461T>G		intron_variant	Intron 1 of 4
LOC105378250	NR_189099.1	n.296-54461T>G		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286069	ENST00000652339.1	n.214-54461T>G		intron_variant	Intron 1 of 4
ENSG00000286069	ENST00000654713.2	n.214+54510T>G		intron_variant	Intron 1 of 2
ENSG00000286069	ENST00000656247.1	n.143+43408T>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15795 AN: 152094 Hom.: 2492 Cov.: 32

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0418

Gnomad ASJ AF: 0.0326

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00994

Gnomad FIN AF: 0.00254

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.00915

Gnomad OTH AF: 0.0850

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

GnomAD4 genome AF: 0.104 AC: 15844 AN: 152212 Hom.: 2504 Cov.: 32 AF XY: 0.101 AC XY: 7481 AN XY: 74432

African (AFR) AF: 0.342 AC: 14196 AN: 41484

American (AMR) AF: 0.0417 AC: 638 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0326 AC: 113 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5190

South Asian (SAS) AF: 0.00974 AC: 47 AN: 4826

European-Finnish (FIN) AF: 0.00254 AC: 27 AN: 10618

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.00915 AC: 622 AN: 68004

Other (OTH) AF: 0.0841 AC: 178 AN: 2116

Alfa AF: 0.0749 Hom.: 247

Bravo AF: 0.118

Asia WGS AF: 0.0240 AC: 86 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	6.8
DANN	Benign	0.76
PhyloP100		0.73

Splicing

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

Other links and lift over

dbSNP: rs10506318; hg19: chr12-54188182;