chr12-63681245-T-C

Position:

• chr12-63681245-T-C

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, non coding transcript 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: ENST00000509615.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.155

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000509615.2	n.239-57421A>G		intron_variant, non_coding_transcript_variant		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;