11-108412434-C-A

Position:

• chr11-108412434-C-A

Variant summary

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

The NM_152587.5(C11orf65):​c.175-5285G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 152,056 control chromosomes in the GnomAD database, including 19,969 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 0.49 (19969 hom., cov: 32)
• Consequence: C11orf65 NM_152587.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212

Genes affected

C11orf65 (HGNC:28519): (chromosome 11 open reading frame 65) Predicted to be involved in negative regulation of mitochondrial fission and negative regulation of protein targeting to mitochondrion. Predicted to be located in cytosol and mitochondrial outer membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.595 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C11orf65	NM_152587.5	c.175-5285G>T		intron_variant		ENST00000393084.6	NP_689800.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C11orf65	ENST00000393084.6	c.175-5285G>T		intron_variant		1	NM_152587.5	ENSP00000376799	P2

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74709 AN: 151938 Hom.: 19960 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.732

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.492 AC: 74737 AN: 152056 Hom.: 19969 Cov.: 32 AF XY: 0.500 AC XY: 37184 AN XY: 74352

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.605

Gnomad4 ASJ AF: 0.639

Gnomad4 EAS AF: 0.385

Gnomad4 SAS AF: 0.604

Gnomad4 FIN AF: 0.630

Gnomad4 NFE AF: 0.568

Gnomad4 OTH AF: 0.540

Alfa AF: 0.557 Hom.: 28980

Bravo AF: 0.477

Asia WGS AF: 0.529 AC: 1836 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.6
DANN	Benign	0.43

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: rs11212617; hg19: chr11-108283161;