rs566164

Positions:

• chr6-109185258-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.220+1167A>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 0.732 in 152,166 control chromosomes in the GnomAD database, including 41,111 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 0.73 (41111 hom., cov: 32)
• Consequence: CCDC162P NR_152435.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.957

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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.812 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC162P	NR_152435.1	n.220+1167A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC162P	ENST00000368966.10	n.137+1167A>G		intron_variant, non_coding_transcript_variant
	ENST00000640771.1	n.218+1167A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.732 AC: 111364 AN: 152048 Hom.: 41068 Cov.: 32

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.797

Gnomad ASJ AF: 0.707

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.832

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.743

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

GnomAD4 genome AF: 0.732 AC: 111457 AN: 152166 Hom.: 41111 Cov.: 32 AF XY: 0.732 AC XY: 54456 AN XY: 74358

Gnomad4 AFR AF: 0.804

Gnomad4 AMR AF: 0.797

Gnomad4 ASJ AF: 0.707

Gnomad4 EAS AF: 0.757

Gnomad4 SAS AF: 0.833

Gnomad4 FIN AF: 0.627

Gnomad4 NFE AF: 0.683

Gnomad4 OTH AF: 0.744

Alfa AF: 0.722 Hom.: 6775

Bravo AF: 0.748

Asia WGS AF: 0.795 AC: 2762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.1
DANN	Benign	0.75

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

Publications

LitVar

Other links and lift over

dbSNP: rs566164; hg19: chr6-109506461;