rs11064896

Variant names:

• chr12-110065082-C-T
• rs11064896
• ENST00000309050.9:n.380+778G>A

Variant summary

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

The ENST00000309050.9(C12orf76):​n.380+778G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0686 in 151,918 control chromosomes in the GnomAD database, including 590 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 0.069 (590 hom., cov: 31)
• Consequence: C12orf76 ENST00000309050.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0620

Genes affected

C12orf76 (HGNC:33790): (chromosome 12 open reading frame 76) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000290863 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C12orf76	NR_148514.2	n.215-5919G>A		intron_variant	Intron 1 of 3
C12orf76	NR_148515.2	n.275+778G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C12orf76	ENST00000309050.9	n.380+778G>A		intron_variant	Intron 2 of 4	2
ENSG00000290863	ENST00000548191.1	n.265+8340G>A		intron_variant	Intron 1 of 1	2
C12orf76	ENST00000548936.1	n.213+8340G>A		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.0686 AC: 10415 AN: 151804 Hom.: 590 Cov.: 31

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0387

Gnomad ASJ AF: 0.0323

Gnomad EAS AF: 0.0854

Gnomad SAS AF: 0.0284

Gnomad FIN AF: 0.0364

Gnomad MID AF: 0.0924

Gnomad NFE AF: 0.0340

Gnomad OTH AF: 0.0605

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

GnomAD4 genome AF: 0.0686 AC: 10421 AN: 151918 Hom.: 590 Cov.: 31 AF XY: 0.0679 AC XY: 5041 AN XY: 74278

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.0386

Gnomad4 ASJ AF: 0.0323

Gnomad4 EAS AF: 0.0856

Gnomad4 SAS AF: 0.0290

Gnomad4 FIN AF: 0.0364

Gnomad4 NFE AF: 0.0341

Gnomad4 OTH AF: 0.0608

Alfa AF: 0.0414 Hom.: 180

Bravo AF: 0.0738

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.46

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs11064896; hg19: chr12-110502887;