rs10876844

Variant names:

• chr12-55656922-C-A
• rs10876844
• ENST00000556606.1:n.83+2791G>T

Variant summary

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

The ENST00000556606.1(ENSG00000258921):​n.83+2791G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 151,876 control chromosomes in the GnomAD database, including 14,514 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 (14514 hom., cov: 31)
• Consequence: ENSG00000258921 ENST00000556606.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.601

Genes affected

ENSG00000258921 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.632 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
ENSG00000258921	ENST00000556606.1	n.83+2791G>T		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65356 AN: 151758 Hom.: 14491 Cov.: 31

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.431 AC: 65419 AN: 151876 Hom.: 14514 Cov.: 31 AF XY: 0.438 AC XY: 32472 AN XY: 74192

Gnomad4 AFR AF: 0.495

Gnomad4 AMR AF: 0.365

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.650

Gnomad4 SAS AF: 0.478

Gnomad4 FIN AF: 0.475

Gnomad4 NFE AF: 0.385

Gnomad4 OTH AF: 0.412

Alfa AF: 0.389 Hom.: 11778

Bravo AF: 0.423

Asia WGS AF: 0.529 AC: 1839 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10876844; hg19: chr12-56050706;