ENST00000547679.1:n.127+9258T>C

Variant names:

• chr12-107106728-T-C
• rs10778534
• ENST00000547679.1:n.127+9258T>C

Variant summary

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

The ENST00000547679.1(ENSG00000257548):​n.127+9258T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 151,880 control chromosomes in the GnomAD database, including 8,367 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 0.31 (8367 hom., cov: 31)
• Consequence: ENSG00000257548 ENST00000547679.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 10 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.427 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+9258T>C		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46493 AN: 151762 Hom.: 8358 Cov.: 31

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.361

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.441

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.306 AC: 46520 AN: 151880 Hom.: 8367 Cov.: 31 AF XY: 0.312 AC XY: 23133 AN XY: 74188

African (AFR) AF: 0.108 AC: 4479 AN: 41448

American (AMR) AF: 0.429 AC: 6545 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1268 AN: 3470

East Asian (EAS) AF: 0.442 AC: 2278 AN: 5154

South Asian (SAS) AF: 0.383 AC: 1843 AN: 4816

European-Finnish (FIN) AF: 0.353 AC: 3715 AN: 10514

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.372 AC: 25291 AN: 67934

Other (OTH) AF: 0.320 AC: 673 AN: 2102

Alfa AF: 0.333 Hom.: 3661

Bravo AF: 0.305

Asia WGS AF: 0.344 AC: 1198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.2
DANN	Benign	0.81
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs10778534; hg19: chr12-107500506;