chr12-55491234-C-T

Position:

• chr12-55491234-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000554049.1(ENSG00000258763):​n.89+1857G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0302 in 151,986 control chromosomes in the GnomAD database, including 116 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 0.030 (116 hom., cov: 32)
• Consequence: ENSG00000258763 ENST00000554049.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.386

Genes affected

ENSG00000258763 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0302 (4590/151986) while in subpopulation NFE AF= 0.0441 (2996/67936). AF 95% confidence interval is 0.0428. There are 116 homozygotes in gnomad4. There are 2296 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 116 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000258763	ENST00000554049.1	n.89+1857G>A		intron_variant		2
ENSG00000258763	ENST00000555138.1	n.125+1857G>A		intron_variant		2
ENSG00000258763	ENST00000556750.5	n.125+1857G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.0302 AC: 4594 AN: 151868 Hom.: 116 Cov.: 32

Gnomad AFR AF: 0.00723

Gnomad AMI AF: 0.00440

Gnomad AMR AF: 0.0185

Gnomad ASJ AF: 0.0259

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0125

Gnomad FIN AF: 0.0763

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0441

Gnomad OTH AF: 0.0230

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

GnomAD4 genome AF: 0.0302 AC: 4590 AN: 151986 Hom.: 116 Cov.: 32 AF XY: 0.0309 AC XY: 2296 AN XY: 74288

Gnomad4 AFR AF: 0.00721

Gnomad4 AMR AF: 0.0184

Gnomad4 ASJ AF: 0.0259

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0125

Gnomad4 FIN AF: 0.0763

Gnomad4 NFE AF: 0.0441

Gnomad4 OTH AF: 0.0228

Alfa AF: 0.0361 Hom.: 13

Bravo AF: 0.0249

Asia WGS AF: 0.00779 AC: 27 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.8
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12828230; hg19: chr12-55885018;