12-127239578-T-C

Variant names:

• chr12-127239578-T-C
• rs3851661
• ENST00000755538.1:n.391-13886T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000755538.1(ENSG00000286791):​n.391-13886T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.434 in 152,076 control chromosomes in the GnomAD database, including 14,448 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 0.43 (14448 hom., cov: 33)
• Consequence: ENSG00000286791 ENST00000755538.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.418
• Publications: 3 publications found

Genes affected

ENSG00000286791 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286791	ENST00000755538.1	n.391-13886T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65996 AN: 151958 Hom.: 14416 Cov.: 33

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.465

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

GnomAD4 genome AF: 0.434 AC: 66070 AN: 152076 Hom.: 14448 Cov.: 33 AF XY: 0.435 AC XY: 32329 AN XY: 74338

African (AFR) AF: 0.452 AC: 18739 AN: 41462

American (AMR) AF: 0.535 AC: 8180 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.526 AC: 1825 AN: 3472

East Asian (EAS) AF: 0.365 AC: 1892 AN: 5182

South Asian (SAS) AF: 0.344 AC: 1659 AN: 4818

European-Finnish (FIN) AF: 0.405 AC: 4268 AN: 10550

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.413 AC: 28083 AN: 67982

Other (OTH) AF: 0.467 AC: 986 AN: 2112

Alfa AF: 0.424 Hom.: 39020

Bravo AF: 0.450

Asia WGS AF: 0.369 AC: 1285 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	4.0
DANN	Benign	0.59
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs3851661; hg19: chr12-127724123;