chr11-108412434-C-A

Variant names:

• chr11-108412434-C-A
• rs11212617
• NM_152587.5:c.175-5285G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 127 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152587.5. 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
	C11orf65	NM_152587.5	MANE Select	c.175-5285G>T		intron	N/A	NP_689800.3
	C11orf65	NM_001330368.2		c.82-5471G>T		intron	N/A	NP_001317297.1
	C11orf65	NM_001351110.2		c.82-5285G>T		intron	N/A	NP_001338039.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C11orf65	ENST00000393084.6	TSL:1 MANE Select	c.175-5285G>T		intron	N/A	ENSP00000376799.1
	C11orf65	ENST00000615746.4	TSL:1	c.175-5285G>T		intron	N/A	ENSP00000483537.1
	C11orf65	ENST00000529391.5	TSL:2	c.175-5285G>T		intron	N/A	ENSP00000436400.1

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

African (AFR) AF: 0.270 AC: 11185 AN: 41466

American (AMR) AF: 0.605 AC: 9237 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.639 AC: 2219 AN: 3470

East Asian (EAS) AF: 0.385 AC: 1993 AN: 5174

South Asian (SAS) AF: 0.604 AC: 2903 AN: 4810

European-Finnish (FIN) AF: 0.630 AC: 6651 AN: 10562

Middle Eastern (MID) AF: 0.723 AC: 211 AN: 292

European-Non Finnish (NFE) AF: 0.568 AC: 38610 AN: 67986

Other (OTH) AF: 0.540 AC: 1140 AN: 2112

Alfa AF: 0.539 Hom.: 70693

Bravo AF: 0.477

Asia WGS AF: 0.529 AC: 1836 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.6
DANN	Benign	0.43
PhyloP100		0.21
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: rs11212617; hg19: chr11-108283161;