ENST00000429614.7:n.467-197G>A

Variant names:

• chr6-109305762-G-A
• rs1008084
• ENST00000429614.7:n.467-197G>A

Variant summary

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

The ENST00000429614.7(ENSG00000293541):​n.467-197G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 151,854 control chromosomes in the GnomAD database, including 12,525 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 0.40 (12525 hom., cov: 33)
• Consequence: ENSG00000293541 ENST00000429614.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.670
• Publications: 25 publications found

Genes affected

ENSG00000293541 (HGNC:):

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]

RNY3P11 (HGNC:50887): (RNY3 pseudogene 11)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC162P	NR_152435.1	n.4168-197G>A		intron_variant	Intron 29 of 45

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293541	ENST00000429614.7	n.467-197G>A		intron_variant	Intron 2 of 3	1
CCDC162P	ENST00000368966.10	n.4200-197G>A		intron_variant	Intron 29 of 45	6
ENSG00000293541	ENST00000422819.6	n.609-197G>A		intron_variant	Intron 3 of 4	2

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60328 AN: 151736 Hom.: 12522 Cov.: 33

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.397 AC: 60347 AN: 151854 Hom.: 12525 Cov.: 33 AF XY: 0.393 AC XY: 29212 AN XY: 74250

African (AFR) AF: 0.371 AC: 15386 AN: 41466

American (AMR) AF: 0.313 AC: 4768 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.436 AC: 1509 AN: 3464

East Asian (EAS) AF: 0.120 AC: 620 AN: 5180

South Asian (SAS) AF: 0.209 AC: 1004 AN: 4802

European-Finnish (FIN) AF: 0.512 AC: 5387 AN: 10520

Middle Eastern (MID) AF: 0.332 AC: 97 AN: 292

European-Non Finnish (NFE) AF: 0.448 AC: 30426 AN: 67870

Other (OTH) AF: 0.391 AC: 825 AN: 2110

Alfa AF: 0.418 Hom.: 18961

Bravo AF: 0.383

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.2
DANN	Benign	0.78
PhyloP100		0.67

Splicing

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

Other links and lift over

dbSNP: rs1008084; hg19: chr6-109626965; COSMIC: COSV63242795;