6-109287294-C-T

Variant names:

• chr6-109287294-C-T
• rs9386791
• ENST00000368966.10:n.3773+776C>T

Variant summary

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

The NR_152435.1(CCDC162P):​n.3744+776C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 152,024 control chromosomes in the GnomAD database, including 19,603 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 0.50 (19603 hom., cov: 32)
• Consequence: CCDC162P NR_152435.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.188

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.565 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC162P	NR_152435.1	n.3744+776C>T		intron_variant	Intron 26 of 45

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC162P	ENST00000368966.10	n.3773+776C>T		intron_variant	Intron 26 of 45	6
CCDC162P	ENST00000615766.4	n.349+776C>T		intron_variant	Intron 3 of 7	5

Frequencies

GnomAD3 genomes AF: 0.504 AC: 76486 AN: 151908 Hom.: 19584 Cov.: 32

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.504 AC: 76549 AN: 152024 Hom.: 19603 Cov.: 32 AF XY: 0.504 AC XY: 37476 AN XY: 74298

Gnomad4 AFR AF: 0.571

Gnomad4 AMR AF: 0.445

Gnomad4 ASJ AF: 0.469

Gnomad4 EAS AF: 0.401

Gnomad4 SAS AF: 0.321

Gnomad4 FIN AF: 0.598

Gnomad4 NFE AF: 0.486

Gnomad4 OTH AF: 0.479

Alfa AF: 0.476 Hom.: 25175

Bravo AF: 0.495

Asia WGS AF: 0.375 AC: 1305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9386791; hg19: chr6-109608497;