rs11966072

chr6-109313625-A-G

Variant summary

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

The NR_152435.1(CCDC162P):n.4571-438A>G variant causes a intron, non coding transcript 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 NR_152435.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.151

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
CCDC162P	NR_152435.1	n.4571-438A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC162P	ENST00000368966.10	n.4603-438A>G		intron_variant, non_coding_transcript_variant
	ENST00000638844.1	n.859-438A>G		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.277

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.411

Gnomad4 NFE AF: 0.342

Gnomad4 OTH AF: 0.260

Alfa AF: 0.311 Hom.: 17631

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11966072; hg19: chr6-109634828;