11-22859013-C-G

Variant names:

• chr11-22859013-C-G
• rs4281481
• NM_001195637.2:c.90+439G>C

Variant summary

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

The NM_001195637.2(CCDC179):​c.90+439G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.368 in 151,606 control chromosomes in the GnomAD database, including 10,779 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 0.37 (10779 hom., cov: 32)
• Consequence: CCDC179 NM_001195637.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50
• Publications: 7 publications found

Genes affected

CCDC179 (HGNC:44653): (coiled-coil domain containing 179)

ENSG00000246225 (HGNC:):

LINC02718 (HGNC:54235): (long intergenic non-protein coding RNA 2718)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001195637.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC179	NM_001195637.2	MANE Select	c.90+439G>C		intron	N/A	NP_001182566.1
	LINC02718	NR_187205.1		n.492+20649C>G		intron	N/A
	LINC02718	NR_187206.1		n.492+20649C>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC179	ENST00000532798.3	TSL:2 MANE Select	c.90+439G>C		intron	N/A	ENSP00000457511.1
	ENSG00000246225	ENST00000499625.1	TSL:5	n.484+20649C>G		intron	N/A
	ENSG00000246225	ENST00000525963.5	TSL:5	n.527-17487C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.368 AC: 55697 AN: 151488 Hom.: 10774 Cov.: 32

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.644

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.368 AC: 55730 AN: 151606 Hom.: 10779 Cov.: 32 AF XY: 0.371 AC XY: 27448 AN XY: 74052

African (AFR) AF: 0.329 AC: 13615 AN: 41372

American (AMR) AF: 0.434 AC: 6628 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 1281 AN: 3468

East Asian (EAS) AF: 0.643 AC: 3305 AN: 5138

South Asian (SAS) AF: 0.564 AC: 2708 AN: 4798

European-Finnish (FIN) AF: 0.252 AC: 2648 AN: 10524

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.358 AC: 24237 AN: 67744

Other (OTH) AF: 0.399 AC: 840 AN: 2104

Alfa AF: 0.336 Hom.: 1049

Bravo AF: 0.376

Asia WGS AF: 0.580 AC: 2010 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.84
DANN	Benign	0.59
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4281481; hg19: chr11-22880559;