rs11966072

Variant names:

• chr6-109313625-A-G
• rs11966072
• ENST00000368966.10:n.4603-438A>G

Variant summary

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

The ENST00000368966.10(CCDC162P):​n.4603-438A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 152,160 control chromosomes in the GnomAD database, including 5,923 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 0.26 (5923 hom., cov: 32)
• Consequence: CCDC162P ENST00000368966.10 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.151
• Publications: 23 publications found

Genes affected

CCDC162P (HGNC:21565): (coiled-coil domain containing 162, pseudogene) This gene is the ortholog of the mouse coiled-coil domain containing 162 gene. This locus is transcribed, but is represented as a unitary pseudogene because there are multiple changes in the coding sequence, including multiple changes that result in premature stop codons, relative to the mouse coding sequence. Transcripts from this locus are expected to encode truncated proteins, and may be candidates for nonsense-mediated decay (NMD). [provided by RefSeq, Sep 2018]

ENSG00000293541 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC162P	NR_152435.1	n.4571-438A>G		intron_variant	Intron 32 of 45

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC162P	ENST00000368966.10	n.4603-438A>G		intron_variant	Intron 32 of 45	6
ENSG00000293541	ENST00000473454.7	n.301+5548A>G		intron_variant	Intron 3 of 11	4
ENSG00000293541	ENST00000506861.1	n.348+3971A>G		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.258 AC: 39168 AN: 152042 Hom.: 5922 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.257 AC: 39174 AN: 152160 Hom.: 5923 Cov.: 32 AF XY: 0.257 AC XY: 19152 AN XY: 74380

African (AFR) AF: 0.127 AC: 5256 AN: 41538

American (AMR) AF: 0.209 AC: 3189 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 961 AN: 3470

East Asian (EAS) AF: 0.113 AC: 583 AN: 5182

South Asian (SAS) AF: 0.152 AC: 732 AN: 4818

European-Finnish (FIN) AF: 0.411 AC: 4347 AN: 10574

Middle Eastern (MID) AF: 0.212 AC: 62 AN: 292

European-Non Finnish (NFE) AF: 0.342 AC: 23249 AN: 67978

Other (OTH) AF: 0.260 AC: 551 AN: 2116

Alfa AF: 0.305 Hom.: 35569

Bravo AF: 0.238

Asia WGS AF: 0.137 AC: 478 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	3.7
DANN	Benign	0.88
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs11966072; hg19: chr6-109634828;