rs4930390

Positions:

• chr11-66792552-A-G

Variant summary

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

The NM_001302084.2(C11orf80):​c.136-3729A>G 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 152,114 control chromosomes in the GnomAD database, including 4,442 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 (4442 hom., cov: 32)
• Consequence: C11orf80 NM_001302084.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240

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=-0.89).
• 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	Protein	UniProt
C11orf80	NM_001302084.2	c.136-3729A>G		intron_variant		ENST00000540737.7	NP_001289013.1
C11orf80	NM_024650.3	c.634-3729A>G		intron_variant			NP_078926.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C11orf80	ENST00000540737.7	c.136-3729A>G		intron_variant		2	NM_001302084.2	ENSP00000444319	A2

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36517 AN: 151996 Hom.: 4445 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: 0.141

Gnomad FIN AF: 0.265

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: 36516 AN: 152114 Hom.: 4442 Cov.: 32 AF XY: 0.238 AC XY: 17721 AN XY: 74358

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: 0.265

Gnomad4 NFE AF: 0.259

Gnomad4 OTH AF: 0.256

Alfa AF: 0.261 Hom.: 10923

Bravo AF: 0.238

Asia WGS AF: 0.156 AC: 545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.8
DANN	Benign	0.65

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: rs4930390; hg19: chr11-66560023;