19-11348063-C-T

Variant names:

• chr19-11348063-C-T
• rs11882629
• NM_001080503.3:c.21+1436C>T

Variant summary

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

The NM_001080503.3(CCDC159):​c.21+1436C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0548 in 449,968 control chromosomes in the GnomAD database, including 1,705 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 0.092 (1281 hom., cov: 32)
  • Exomes 𝑓: 0.036 (424 hom.)
• Consequence: CCDC159 NM_001080503.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0780
• Publications: 2 publications found

Genes affected

CCDC159 (HGNC:26996): (coiled-coil domain containing 159)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.24 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC159	NM_001080503.3	c.21+1436C>T		intron_variant	Intron 1 of 10	ENST00000458408.6	NP_001073972.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC159	ENST00000458408.6	c.21+1436C>T		intron_variant	Intron 1 of 10	5	NM_001080503.3	ENSP00000402239.1

Frequencies

GnomAD3 genomes AF: 0.0921 AC: 14013 AN: 152110 Hom.: 1285 Cov.: 32

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.0418

Gnomad ASJ AF: 0.0170

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0172

Gnomad FIN AF: 0.0347

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0382

Gnomad OTH AF: 0.0588

GnomAD4 exome AF: 0.0357 AC: 10638 AN: 297740 Hom.: 424 AF XY: 0.0326 AC XY: 5534 AN XY: 169918

African (AFR) AF: 0.246 AC: 2021 AN: 8204

American (AMR) AF: 0.0253 AC: 656 AN: 25946

Ashkenazi Jewish (ASJ) AF: 0.0181 AC: 191 AN: 10562

East Asian (EAS) AF: 0.000218 AC: 2 AN: 9184

South Asian (SAS) AF: 0.0170 AC: 993 AN: 58556

European-Finnish (FIN) AF: 0.0365 AC: 465 AN: 12742

Middle Eastern (MID) AF: 0.0290 AC: 48 AN: 1656

European-Non Finnish (NFE) AF: 0.0364 AC: 5710 AN: 157026

Other (OTH) AF: 0.0398 AC: 552 AN: 13864

GnomAD4 genome AF: 0.0921 AC: 14022 AN: 152228 Hom.: 1281 Cov.: 32 AF XY: 0.0902 AC XY: 6713 AN XY: 74406

African (AFR) AF: 0.244 AC: 10119 AN: 41506

American (AMR) AF: 0.0416 AC: 636 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0170 AC: 59 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5188

South Asian (SAS) AF: 0.0170 AC: 82 AN: 4822

European-Finnish (FIN) AF: 0.0347 AC: 368 AN: 10598

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0382 AC: 2596 AN: 68034

Other (OTH) AF: 0.0596 AC: 126 AN: 2114

Alfa AF: 0.0491 Hom.: 510

Bravo AF: 0.0997

Asia WGS AF: 0.0210 AC: 73 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.9
DANN	Benign	0.72
PhyloP100		-0.078
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: rs11882629; hg19: chr19-11458739;