12-111757172-T-C

Position:

• chr12-111757172-T-C

Variant summary

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

The ENST00000546840.3(ENSG00000257767):​c.102+1427T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 338,786 control chromosomes in the GnomAD database, including 37,303 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 0.46 (20271 hom., cov: 32)
  • Exomes 𝑓: 0.38 (17032 hom.)
• Consequence: ENSG00000257767 ENST00000546840.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.76

Genes affected

ENSG00000257767 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.879 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.111757172T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000257767	ENST00000546840.3	c.102+1427T>C		intron_variant		5		ENSP00000450353.4

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69328 AN: 151904 Hom.: 20216 Cov.: 32

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.900

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.434

GnomAD4 exome AF: 0.383 AC: 71608 AN: 186764 Hom.: 17032 AF XY: 0.409 AC XY: 41811 AN XY: 102228

Gnomad4 AFR exome AF: 0.774

Gnomad4 AMR exome AF: 0.448

Gnomad4 ASJ exome AF: 0.166

Gnomad4 EAS exome AF: 0.907

Gnomad4 SAS exome AF: 0.581

Gnomad4 FIN exome AF: 0.248

Gnomad4 NFE exome AF: 0.274

Gnomad4 OTH exome AF: 0.335

GnomAD4 genome AF: 0.457 AC: 69448 AN: 152022 Hom.: 20271 Cov.: 32 AF XY: 0.461 AC XY: 34232 AN XY: 74304

Gnomad4 AFR AF: 0.781

Gnomad4 AMR AF: 0.433

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.900

Gnomad4 SAS AF: 0.599

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.274

Gnomad4 OTH AF: 0.433

Alfa AF: 0.309 Hom.: 8951

Bravo AF: 0.486

Asia WGS AF: 0.712 AC: 2477 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.10
DANN	Benign	0.33

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs737280; hg19: chr12-112194976; COSMIC: COSV58158260; COSMIC: COSV58158260;