chr12-53867976-C-T

Variant names:

• chr12-53867976-C-T
• rs10506325
• ENST00000652339.1:n.509+7098C>T

Variant summary

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

The NR_189097.1(LOC105378250):​n.398+17564C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 151,998 control chromosomes in the GnomAD database, including 14,474 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 0.42 (14474 hom., cov: 31)
• Consequence: LOC105378250 NR_189097.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.308

Genes affected

ENSG00000286069 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378250	NR_189097.1	n.398+17564C>T		intron_variant	Intron 2 of 2
LOC105378250	NR_189098.1	n.497-7179C>T		intron_variant	Intron 3 of 4
LOC105378250	NR_189099.1	n.591+7098C>T		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286069	ENST00000652339.1	n.509+7098C>T		intron_variant	Intron 4 of 4
ENSG00000286069	ENST00000654713.1	n.317+17564C>T		intron_variant	Intron 2 of 2
ENSG00000286069	ENST00000656247.1	n.344+17564C>T		intron_variant	Intron 3 of 3
ENSG00000286069	ENST00000663306.1	n.480-7179C>T		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64506 AN: 151880 Hom.: 14462 Cov.: 31

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.425 AC: 64553 AN: 151998 Hom.: 14474 Cov.: 31 AF XY: 0.415 AC XY: 30857 AN XY: 74290

Gnomad4 AFR AF: 0.563

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.420

Gnomad4 EAS AF: 0.228

Gnomad4 SAS AF: 0.359

Gnomad4 FIN AF: 0.320

Gnomad4 NFE AF: 0.409

Gnomad4 OTH AF: 0.382

Alfa AF: 0.409 Hom.: 2086

Bravo AF: 0.426

Asia WGS AF: 0.300 AC: 1049 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	4.6
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10506325; hg19: chr12-54261760;