rs479777

Variant names:

• chr11-64340005-T-C
• rs479777
• ENST00000690790.2:n.150A>G

Variant summary

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

The NR_188518.1(LOC102723878):​n.326A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 152,072 control chromosomes in the GnomAD database, including 6,441 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 0.27 (6441 hom., cov: 32)
• Consequence: LOC102723878 NR_188518.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261

Genes affected

ENSG00000236935 (HGNC:):

CCDC88B (HGNC:26757): (coiled-coil domain containing 88B) This gene encodes a member of the hook-related protein family. Members of this family are characterized by an N-terminal potential microtubule binding domain, a central coiled-coiled and a C-terminal Hook-related domain. The encoded protein may be involved in linking organelles to microtubules. [provided by RefSeq, Oct 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723878	NR_188518.1	n.326A>G		non_coding_transcript_exon_variant	Exon 2 of 4
LOC102723878	NR_188519.1	n.151A>G		non_coding_transcript_exon_variant	Exon 1 of 3
LOC102723878	NR_188520.1	n.151A>G		non_coding_transcript_exon_variant	Exon 1 of 3
CCDC88B	NM_032251.6	c.-262T>C		upstream_gene_variant		ENST00000356786.10	NP_115627.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000236935	ENST00000690790.2	n.150A>G		non_coding_transcript_exon_variant	Exon 1 of 3
CCDC88B	ENST00000356786.10	c.-262T>C		upstream_gene_variant		1	NM_032251.6	ENSP00000349238.5
CCDC88B	ENST00000463837.5	n.-218T>C		upstream_gene_variant		2

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41367 AN: 151956 Hom.: 6431 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.272 AC: 41408 AN: 152072 Hom.: 6441 Cov.: 32 AF XY: 0.276 AC XY: 20475 AN XY: 74310

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.333

Gnomad4 ASJ AF: 0.373

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.379

Gnomad4 NFE AF: 0.336

Gnomad4 OTH AF: 0.253

Alfa AF: 0.316 Hom.: 2748

Bravo AF: 0.263

Asia WGS AF: 0.247 AC: 859 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.1
DANN	Benign	0.50

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs479777; hg19: chr11-64107477;