chr11-64340005-T-C

Variant names:

• chr11-64340005-T-C
• rs479777
• ENST00000690790.3:n.199A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000690790.3(ENSG00000236935):​n.199A>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: ENSG00000236935 ENST00000690790.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261
• Publications: 49 publications found

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

Our verdict: Benign. The variant received -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
CCDC88B	ENST00000356786.10	c.-262T>C		upstream_gene_variant		1	NM_032251.6	ENSP00000349238.5

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

African (AFR) AF: 0.122 AC: 5080 AN: 41522

American (AMR) AF: 0.333 AC: 5083 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.373 AC: 1295 AN: 3470

East Asian (EAS) AF: 0.186 AC: 958 AN: 5162

South Asian (SAS) AF: 0.266 AC: 1280 AN: 4820

European-Finnish (FIN) AF: 0.379 AC: 3997 AN: 10554

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.336 AC: 22815 AN: 67960

Other (OTH) AF: 0.253 AC: 534 AN: 2112

Alfa AF: 0.311 Hom.: 13338

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
PhyloP100		-0.26
PromoterAI		-0.069	Neutral

Splicing

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

Other links and lift over

dbSNP: rs479777; hg19: chr11-64107477;