12-107111862-C-T

Position:

• chr12-107111862-C-T

Variant summary

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

The ENST00000547679.1(ENSG00000257548):​n.128-10111C>T 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 0.495 in 151,986 control chromosomes in the GnomAD database, including 19,771 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 0.50 (19771 hom., cov: 32)
• Consequence: ENST00000547679.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.705 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
	ENST00000547679.1	n.128-10111C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.495 AC: 75220 AN: 151868 Hom.: 19756 Cov.: 32

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.542

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.495 AC: 75267 AN: 151986 Hom.: 19771 Cov.: 32 AF XY: 0.499 AC XY: 37096 AN XY: 74286

Gnomad4 AFR AF: 0.310

Gnomad4 AMR AF: 0.586

Gnomad4 ASJ AF: 0.477

Gnomad4 EAS AF: 0.725

Gnomad4 SAS AF: 0.568

Gnomad4 FIN AF: 0.512

Gnomad4 NFE AF: 0.563

Gnomad4 OTH AF: 0.517

Alfa AF: 0.554 Hom.: 31763

Bravo AF: 0.493

Asia WGS AF: 0.596 AC: 2072 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.50
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10861709; hg19: chr12-107505640;