rs10778456

chr12-106054524-C-T

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, non coding transcript 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: ENST00000546699.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000546699.1	n.154-2349G>A		intron_variant, non_coding_transcript_variant		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;