12-63681245-T-C

Variant names:

• chr12-63681245-T-C
• rs11504159
• ENST00000509615.2:n.239-57421A>G

Variant summary

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

The ENST00000509615.2(ENSG00000249753):​n.239-57421A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.367 in 151,694 control chromosomes in the GnomAD database, including 10,299 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 0.37 (10299 hom., cov: 30)
• Consequence: ENSG00000249753 ENST00000509615.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.155

Genes affected

ENSG00000249753 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.404 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
ENSG00000249753	ENST00000509615.2	n.239-57421A>G		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55644 AN: 151576 Hom.: 10273 Cov.: 30

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.367 AC: 55718 AN: 151694 Hom.: 10299 Cov.: 30 AF XY: 0.363 AC XY: 26876 AN XY: 74122

Gnomad4 AFR AF: 0.406

Gnomad4 AMR AF: 0.413

Gnomad4 ASJ AF: 0.430

Gnomad4 EAS AF: 0.269

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.359

Gnomad4 OTH AF: 0.371

Alfa AF: 0.354 Hom.: 1224

Bravo AF: 0.379

Asia WGS AF: 0.259 AC: 903 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.8
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11504159; hg19: chr12-64075025;