rs35424364

chr6-109322402-A-AT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NR_152435.1(CCDC162P):n.5060+5438dup 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 0.875 in 151,988 control chromosomes in the GnomAD database, including 58,495 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.87 (58495 hom., cov: 0)
• Consequence: CCDC162P NR_152435.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.219

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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.955 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC162P	NR_152435.1	n.5060+5438dup		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC162P	ENST00000368966.10	n.5092+5438dup		intron_variant, non_coding_transcript_variant
	ENST00000638844.1	n.1348+5438dup		intron_variant, non_coding_transcript_variant		5
	ENST00000506861.1	n.349-6597dup		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.875 AC: 132857 AN: 151870 Hom.: 58446 Cov.: 0

Gnomad AFR AF: 0.963

Gnomad AMI AF: 0.743

Gnomad AMR AF: 0.849

Gnomad ASJ AF: 0.826

Gnomad EAS AF: 0.857

Gnomad SAS AF: 0.845

Gnomad FIN AF: 0.921

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.828

Gnomad OTH AF: 0.863

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

GnomAD4 genome AF: 0.875 AC: 132963 AN: 151988 Hom.: 58495 Cov.: 0 AF XY: 0.877 AC XY: 65173 AN XY: 74292

Gnomad4 AFR AF: 0.963

Gnomad4 AMR AF: 0.849

Gnomad4 ASJ AF: 0.826

Gnomad4 EAS AF: 0.857

Gnomad4 SAS AF: 0.844

Gnomad4 FIN AF: 0.921

Gnomad4 NFE AF: 0.828

Gnomad4 OTH AF: 0.864

Alfa AF: 0.856 Hom.: 6015

Bravo AF: 0.875

Asia WGS AF: 0.873 AC: 3021 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35424364; hg19: chr6-109643605;