6-109277761-G-A

Variant names:

• chr6-109277761-G-A
• rs13210693
• ENST00000368966.10:n.3277-4806G>A

Variant summary

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

The ENST00000368966.10(CCDC162P):​n.3277-4806G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.605 in 151,974 control chromosomes in the GnomAD database, including 29,614 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 0.61 (29614 hom., cov: 31)
• Consequence: CCDC162P ENST00000368966.10 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.581
• Publications: 19 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.827 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC162P	NR_152435.1	n.3360-4806G>A		intron_variant	Intron 23 of 45

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC162P	ENST00000368966.10	n.3277-4806G>A		intron_variant	Intron 22 of 45	6
ENSG00000293470	ENST00000713557.1	n.392-4806G>A		intron_variant	Intron 3 of 3
ENSG00000300459	ENST00000771980.1	n.1225+11966C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.605 AC: 91868 AN: 151856 Hom.: 29579 Cov.: 31

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.642

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.605 AC: 91950 AN: 151974 Hom.: 29614 Cov.: 31 AF XY: 0.604 AC XY: 44891 AN XY: 74276

African (AFR) AF: 0.834 AC: 34600 AN: 41466

American (AMR) AF: 0.491 AC: 7484 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.579 AC: 2007 AN: 3466

East Asian (EAS) AF: 0.492 AC: 2540 AN: 5160

South Asian (SAS) AF: 0.356 AC: 1711 AN: 4808

European-Finnish (FIN) AF: 0.642 AC: 6770 AN: 10540

Middle Eastern (MID) AF: 0.517 AC: 151 AN: 292

European-Non Finnish (NFE) AF: 0.516 AC: 35042 AN: 67972

Other (OTH) AF: 0.566 AC: 1193 AN: 2108

Alfa AF: 0.536 Hom.: 65148

Bravo AF: 0.607

Asia WGS AF: 0.448 AC: 1559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.5
DANN	Benign	0.64
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs13210693; hg19: chr6-109598964;