rs566164

Variant names:

• chr6-109185258-A-G
• rs566164
• ENST00000368966.10:n.137+1167A>G

Variant summary

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

The NR_152435.1(CCDC162P):​n.220+1167A>G variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.957
• Publications: 3 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]

ENSG00000293470 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_152435.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC162P	NR_152435.1		n.220+1167A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC162P	ENST00000368966.10	TSL:6	n.137+1167A>G		intron	N/A
	ENSG00000293470	ENST00000640771.1	TSL:5	n.218+1167A>G		intron	N/A

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

African (AFR) AF: 0.804 AC: 33393 AN: 41518

American (AMR) AF: 0.797 AC: 12189 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.707 AC: 2453 AN: 3470

East Asian (EAS) AF: 0.757 AC: 3924 AN: 5182

South Asian (SAS) AF: 0.833 AC: 4012 AN: 4814

European-Finnish (FIN) AF: 0.627 AC: 6628 AN: 10568

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.683 AC: 46439 AN: 68000

Other (OTH) AF: 0.744 AC: 1572 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.1
DANN	Benign	0.75
PhyloP100		0.96

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: rs566164; hg19: chr6-109506461;