rs13210693

chr6-109277761-G-A

Variant summary

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

The NR_152435.1(CCDC162P):n.3360-4806G>A 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 0.605 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 NR_152435.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.581

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=-0.99).
• 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/exons	MANE	UniProt
CCDC162P	NR_152435.1	n.3360-4806G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC162P	ENST00000368966.10	n.3277-4806G>A		intron_variant, non_coding_transcript_variant
	ENST00000713557.1	n.392-4806G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.834

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.579

Gnomad4 EAS AF: 0.492

Gnomad4 SAS AF: 0.356

Gnomad4 FIN AF: 0.642

Gnomad4 NFE AF: 0.516

Gnomad4 OTH AF: 0.566

Alfa AF: 0.516 Hom.: 40314

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13210693; hg19: chr6-109598964;