rs652311

Positions:

• chr11-108369342-G-A
• chr11-108369342-G-C

Variant summary

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

The NM_001330368.2(C11orf65):​c.640+16578C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.538 in 151,920 control chromosomes in the GnomAD database, including 22,546 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 0.54 (22546 hom., cov: 31)
• Consequence: C11orf65 NM_001330368.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01

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]

C11orf65 (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 (SAS) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C11orf65	NM_001330368.2	c.640+16578C>T		intron_variant			NP_001317297.1
C11orf65	NM_001351110.2	c.694+16578C>T		intron_variant			NP_001338039.1
C11orf65	XM_047426458.1	c.731+23866C>T		intron_variant			XP_047282414.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C11orf65	ENST00000615746.4	c.*2-13233C>T		intron_variant		1		ENSP00000483537.1
C11orf65	ENST00000525729.5	c.640+16578C>T		intron_variant		2		ENSP00000433395.1
C11orf65	ENST00000524755.5	c.224+23866C>T		intron_variant		3		ENSP00000432827.1

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81640 AN: 151804 Hom.: 22533 Cov.: 31

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.436

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.631

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.571

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

GnomAD4 genome AF: 0.538 AC: 81681 AN: 151920 Hom.: 22546 Cov.: 31 AF XY: 0.546 AC XY: 40495 AN XY: 74230

Gnomad4 AFR AF: 0.416

Gnomad4 AMR AF: 0.623

Gnomad4 ASJ AF: 0.641

Gnomad4 EAS AF: 0.437

Gnomad4 SAS AF: 0.651

Gnomad4 FIN AF: 0.631

Gnomad4 NFE AF: 0.569

Gnomad4 OTH AF: 0.572

Alfa AF: 0.544 Hom.: 3428

Bravo AF: 0.529

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.7
DANN	Benign	0.42

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: rs652311; hg19: chr11-108240069;