ENST00000552856.1:n.296-40909C>T

Variant names:

• chr12-75818439-G-A
• rs10879987
• ENST00000552856.1:n.296-40909C>T

Variant summary

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

The ENST00000552856.1(ENSG00000258077):​n.296-40909C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 151,698 control chromosomes in the GnomAD database, including 9,530 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 0.34 (9530 hom., cov: 31)
• Consequence: ENSG00000258077 ENST00000552856.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.128
• Publications: 2 publications found

Genes affected

ENSG00000258077 (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 = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369844	XR_007063374.1	n.236+16094C>T		intron_variant	Intron 1 of 6
LOC105369844	XR_007063375.1	n.236+16094C>T		intron_variant	Intron 1 of 15
LOC105369844	XR_007063376.1	n.236+16094C>T		intron_variant	Intron 1 of 7
LOC105369844	XR_007063377.1	n.236+16094C>T		intron_variant	Intron 1 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000258077	ENST00000552856.1	n.296-40909C>T		intron_variant	Intron 1 of 4	3
ENSG00000258077	ENST00000741358.1	n.83+7284C>T		intron_variant	Intron 1 of 6
ENSG00000258077	ENST00000741359.1	n.83+7284C>T		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51030 AN: 151578 Hom.: 9542 Cov.: 31

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.336 AC: 50991 AN: 151698 Hom.: 9530 Cov.: 31 AF XY: 0.338 AC XY: 25024 AN XY: 74120

African (AFR) AF: 0.176 AC: 7295 AN: 41376

American (AMR) AF: 0.324 AC: 4939 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1322 AN: 3460

East Asian (EAS) AF: 0.314 AC: 1621 AN: 5164

South Asian (SAS) AF: 0.315 AC: 1510 AN: 4796

European-Finnish (FIN) AF: 0.476 AC: 4996 AN: 10496

Middle Eastern (MID) AF: 0.438 AC: 128 AN: 292

European-Non Finnish (NFE) AF: 0.414 AC: 28085 AN: 67848

Other (OTH) AF: 0.355 AC: 748 AN: 2110

Alfa AF: 0.364 Hom.: 1475

Bravo AF: 0.318

Asia WGS AF: 0.297 AC: 1036 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.4
DANN	Benign	0.70
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs10879987; hg19: chr12-76212219;