rs10778456

Variant names:

• chr12-106054524-C-T
• rs10778456
• ENST00000546699.1:n.154-2349G>A

Variant summary

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

The ENST00000546699.1(ENSG00000257890):​n.154-2349G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 151,878 control chromosomes in the GnomAD database, including 14,521 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 (14521 hom., cov: 31)
• Consequence: ENSG00000257890 ENST00000546699.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

Genes affected

ENSG00000257890 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.537 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
ENSG00000257890	ENST00000546699.1	n.154-2349G>A		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.428 AC: 64957 AN: 151760 Hom.: 14498 Cov.: 31

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.428 AC: 65025 AN: 151878 Hom.: 14521 Cov.: 31 AF XY: 0.428 AC XY: 31751 AN XY: 74202

Gnomad4 AFR AF: 0.289

Gnomad4 AMR AF: 0.547

Gnomad4 ASJ AF: 0.422

Gnomad4 EAS AF: 0.421

Gnomad4 SAS AF: 0.435

Gnomad4 FIN AF: 0.436

Gnomad4 NFE AF: 0.486

Gnomad4 OTH AF: 0.418

Alfa AF: 0.468 Hom.: 7950

Bravo AF: 0.428

Asia WGS AF: 0.434 AC: 1507 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.15
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10778456; hg19: chr12-106448302;