ENST00000547679.1:n.127+11877G>A

Variant names:

• chr12-107109347-G-A
• rs4262808
• ENST00000547679.1:n.127+11877G>A

Variant summary

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

The ENST00000547679.1(ENSG00000257548):​n.127+11877G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.507 in 151,676 control chromosomes in the GnomAD database, including 20,362 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 0.51 (20362 hom., cov: 30)
• Consequence: ENSG00000257548 ENST00000547679.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.434
• Publications: 3 publications found

Genes affected

ENSG00000257548 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.702 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
ENSG00000257548	ENST00000547679.1	n.127+11877G>A		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.507 AC: 76876 AN: 151558 Hom.: 20339 Cov.: 30

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.507 AC: 76945 AN: 151676 Hom.: 20362 Cov.: 30 AF XY: 0.511 AC XY: 37867 AN XY: 74064

African (AFR) AF: 0.350 AC: 14466 AN: 41332

American (AMR) AF: 0.592 AC: 9024 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.477 AC: 1655 AN: 3468

East Asian (EAS) AF: 0.722 AC: 3697 AN: 5122

South Asian (SAS) AF: 0.579 AC: 2777 AN: 4800

European-Finnish (FIN) AF: 0.511 AC: 5352 AN: 10482

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.564 AC: 38284 AN: 67926

Other (OTH) AF: 0.522 AC: 1101 AN: 2108

Alfa AF: 0.547 Hom.: 11661

Bravo AF: 0.508

Asia WGS AF: 0.605 AC: 2103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.6
DANN	Benign	0.82
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs4262808; hg19: chr12-107503125;