rs35424364

Variant names:

• chr6-109322402-A-AT
• rs35424364
• ENST00000368966.10:n.5092+5434_5092+5435insT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000473454.7(ENSG00000293541):​n.302-13966_302-13965insT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.87 (58495 hom., cov: 0)
• Consequence: ENSG00000293541 ENST00000473454.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.219
• Publications: 6 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]

ENSG00000293541 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.955 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000473454.7. 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.5060+5438dupT		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC162P	ENST00000368966.10	TSL:6	n.5092+5434_5092+5435insT		intron	N/A
	ENSG00000293541	ENST00000473454.7	TSL:4	n.302-13966_302-13965insT		intron	N/A
	ENSG00000293541	ENST00000506861.1	TSL:4	n.349-6601_349-6600insT		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.875 AC: 132857 AN: 151870 Hom.: 58446 Cov.: 0

Gnomad AFR AF: 0.963

Gnomad AMI AF: 0.743

Gnomad AMR AF: 0.849

Gnomad ASJ AF: 0.826

Gnomad EAS AF: 0.857

Gnomad SAS AF: 0.845

Gnomad FIN AF: 0.921

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.828

Gnomad OTH AF: 0.863

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

GnomAD4 genome AF: 0.875 AC: 132963 AN: 151988 Hom.: 58495 Cov.: 0 AF XY: 0.877 AC XY: 65173 AN XY: 74292

African (AFR) AF: 0.963 AC: 39981 AN: 41512

American (AMR) AF: 0.849 AC: 12957 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.826 AC: 2866 AN: 3470

East Asian (EAS) AF: 0.857 AC: 4432 AN: 5172

South Asian (SAS) AF: 0.844 AC: 4072 AN: 4826

European-Finnish (FIN) AF: 0.921 AC: 9637 AN: 10460

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.828 AC: 56265 AN: 67966

Other (OTH) AF: 0.864 AC: 1824 AN: 2110

Alfa AF: 0.856 Hom.: 6015

Bravo AF: 0.875

Asia WGS AF: 0.873 AC: 3021 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs35424364; hg19: chr6-109643605;