11-66783531-G-C

Variant summary

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

The NM_001302084.2(C11orf80):c.26-4629G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 152,022 control chromosomes in the GnomAD database, including 4,448 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 0.24 (4448 hom., cov: 32)
• Consequence: C11orf80 NM_001302084.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.780

Genes affected

C11orf80 (HGNC:26197): (TOP6B like initiator of meiotic double strand breaks) Predicted to be involved in meiotic DNA double-strand break formation and reciprocal meiotic recombination. Predicted to be located in chromosome. Implicated in gestational trophoblastic neoplasm. [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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C11orf80	NM_001302084.2	c.26-4629G>C		intron_variant		ENST00000540737.7
C11orf80	NM_024650.3	c.524-4629G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C11orf80	ENST00000540737.7	c.26-4629G>C		intron_variant		2	NM_001302084.2	A2

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36515 AN: 151904 Hom.: 4451 Cov.: 32

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.240 AC: 36514 AN: 152022 Hom.: 4448 Cov.: 32 AF XY: 0.239 AC XY: 17736 AN XY: 74316

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.313

Gnomad4 EAS AF: 0.161

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.267

Gnomad4 NFE AF: 0.259

Gnomad4 OTH AF: 0.256

Alfa AF: 0.241 Hom.: 2529

Bravo AF: 0.238

Asia WGS AF: 0.156 AC: 546 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.23
Dann	Benign	0.51

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: rs10896135; hg19: chr11-66551002;