6-109303734-G-A

Position:

• chr6-109303734-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.4168-2225G>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 0.44 in 151,918 control chromosomes in the GnomAD database, including 15,257 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 0.44 (15257 hom., cov: 31)
• Consequence: CCDC162P NR_152435.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.859

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC162P	NR_152435.1	n.4168-2225G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC162P	ENST00000368966.10	n.4200-2225G>A		intron_variant, non_coding_transcript_variant
	ENST00000638844.1	n.456-2225G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.440 AC: 66794 AN: 151800 Hom.: 15235 Cov.: 31

Gnomad AFR AF: 0.570

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.440 AC: 66860 AN: 151918 Hom.: 15257 Cov.: 31 AF XY: 0.442 AC XY: 32836 AN XY: 74222

Gnomad4 AFR AF: 0.570

Gnomad4 AMR AF: 0.368

Gnomad4 ASJ AF: 0.425

Gnomad4 EAS AF: 0.392

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.491

Gnomad4 NFE AF: 0.385

Gnomad4 OTH AF: 0.415

Alfa AF: 0.377 Hom.: 23260

Bravo AF: 0.434

Asia WGS AF: 0.367 AC: 1276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.5
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9784763; hg19: chr6-109624937;