12-56104119-C-T

Position:

• chr12-56104119-C-T

Variant summary

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

The ENST00000548861.2(ENSG00000257411):​c.32-2469C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 151,978 control chromosomes in the GnomAD database, including 6,655 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 0.29 (6655 hom., cov: 31)
• Consequence: ENSG00000257411 ENST00000548861.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19

Genes affected

ENSG00000257411 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105369782	XR_944995.4	n.132+169G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000257411	ENST00000548861.2	c.32-2469C>T		intron_variant		5		ENSP00000449770.3

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43516 AN: 151860 Hom.: 6642 Cov.: 31

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.450

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.287 AC: 43563 AN: 151978 Hom.: 6655 Cov.: 31 AF XY: 0.286 AC XY: 21207 AN XY: 74270

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.342

Gnomad4 SAS AF: 0.271

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.336

Gnomad4 OTH AF: 0.315

Alfa AF: 0.283 Hom.: 1637

Bravo AF: 0.284

Asia WGS AF: 0.321 AC: 1118 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	13
DANN	Benign	0.84

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: rs3759094; hg19: chr12-56497903;