rs11064896

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000309050.9. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C12orf76	NR_148514.2		n.215-5919G>A		intron	N/A
	C12orf76	NR_148515.2		n.275+778G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C12orf76	ENST00000309050.9	TSL:2	n.380+778G>A		intron	N/A
	ENSG00000290863	ENST00000548191.1	TSL:2	n.265+8340G>A		intron	N/A
	C12orf76	ENST00000548936.1	TSL:4	n.213+8340G>A		intron	N/A

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

African (AFR) AF: 0.152 AC: 6278 AN: 41406

American (AMR) AF: 0.0386 AC: 589 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.0323 AC: 112 AN: 3468

East Asian (EAS) AF: 0.0856 AC: 443 AN: 5178

South Asian (SAS) AF: 0.0290 AC: 140 AN: 4822

European-Finnish (FIN) AF: 0.0364 AC: 382 AN: 10508

Middle Eastern (MID) AF: 0.0925 AC: 27 AN: 292

European-Non Finnish (NFE) AF: 0.0341 AC: 2315 AN: 67982

Other (OTH) AF: 0.0608 AC: 128 AN: 2104

Alfa AF: 0.0443 Hom.: 300

Bravo AF: 0.0738

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.46
PhyloP100		-0.062
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11064896; hg19: chr12-110502887;