rs9374080

Positions:

• chr6-109295217-T-C

Variant summary

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

The NR_152435.1(CCDC162P):​n.3863-310T>C 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 0.393 in 152,054 control chromosomes in the GnomAD database, including 12,296 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 0.39 (12296 hom., cov: 32)
• Consequence: CCDC162P NR_152435.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.33

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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC162P	NR_152435.1	n.3863-310T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC162P	ENST00000368966.10	n.3895-310T>C		intron_variant, non_coding_transcript_variant
	ENST00000638844.1	n.151-310T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59721 AN: 151936 Hom.: 12293 Cov.: 32

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.393 AC: 59733 AN: 152054 Hom.: 12296 Cov.: 32 AF XY: 0.389 AC XY: 28915 AN XY: 74322

Gnomad4 AFR AF: 0.352

Gnomad4 AMR AF: 0.312

Gnomad4 ASJ AF: 0.436

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.515

Gnomad4 NFE AF: 0.449

Gnomad4 OTH AF: 0.387

Alfa AF: 0.417 Hom.: 16697

Bravo AF: 0.378

Asia WGS AF: 0.191 AC: 666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.6
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9374080; hg19: chr6-109616420;