rs10879987

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000552856.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000258077	ENST00000552856.1	TSL:3	n.296-40909C>T		intron	N/A
	ENSG00000258077	ENST00000741358.1		n.83+7284C>T		intron	N/A
	ENSG00000258077	ENST00000741359.1		n.83+7284C>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10879987;

hg19: chr12-76212219;