ENST00000429614.6:n.323-2225G>A

Variant names:

• chr6-109303734-G-A
• rs9784763
• ENST00000429614.7:n.467-2225G>A

Variant summary

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

The ENST00000429614.7(ENSG00000293541):​n.467-2225G>A variant causes a intron 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: ENSG00000293541 ENST00000429614.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.859
• Publications: 4 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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000429614.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC162P	NR_152435.1		n.4168-2225G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293541	ENST00000429614.7	TSL:1	n.467-2225G>A		intron	N/A
	CCDC162P	ENST00000368966.10	TSL:6	n.4200-2225G>A		intron	N/A
	ENSG00000293541	ENST00000422819.6	TSL:2	n.609-2225G>A		intron	N/A

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

African (AFR) AF: 0.570 AC: 23611 AN: 41432

American (AMR) AF: 0.368 AC: 5612 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1475 AN: 3468

East Asian (EAS) AF: 0.392 AC: 2025 AN: 5162

South Asian (SAS) AF: 0.304 AC: 1466 AN: 4816

European-Finnish (FIN) AF: 0.491 AC: 5166 AN: 10530

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.385 AC: 26192 AN: 67944

Other (OTH) AF: 0.415 AC: 875 AN: 2106

Alfa AF: 0.389 Hom.: 34629

Bravo AF: 0.434

Asia WGS AF: 0.367 AC: 1276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.5
DANN	Benign	0.18
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs9784763; hg19: chr6-109624937;