12-78362131-G-A

Variant names:

• chr12-78362131-G-A
• rs11109504
• ENST00000552230.5:n.162+9451G>A

Variant summary

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

The ENST00000552230.5(ENSG00000258084):​n.162+9451G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 151,952 control chromosomes in the GnomAD database, including 10,285 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 0.36 (10285 hom., cov: 32)
• Consequence: ENSG00000258084 ENST00000552230.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.726
• Publications: 3 publications found

Genes affected

ENSG00000258084 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.411 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
ENSG00000258084	ENST00000552230.5	n.162+9451G>A		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54622 AN: 151834 Hom.: 10285 Cov.: 32

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.360 AC: 54639 AN: 151952 Hom.: 10285 Cov.: 32 AF XY: 0.363 AC XY: 26998 AN XY: 74284

African (AFR) AF: 0.279 AC: 11558 AN: 41458

American (AMR) AF: 0.287 AC: 4387 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 959 AN: 3468

East Asian (EAS) AF: 0.302 AC: 1558 AN: 5162

South Asian (SAS) AF: 0.323 AC: 1559 AN: 4824

European-Finnish (FIN) AF: 0.488 AC: 5147 AN: 10554

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.415 AC: 28212 AN: 67914

Other (OTH) AF: 0.339 AC: 715 AN: 2112

Alfa AF: 0.377 Hom.: 14081

Bravo AF: 0.340

Asia WGS AF: 0.312 AC: 1084 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.16
DANN	Benign	0.40
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs11109504; hg19: chr12-78755911;