6-109295217-T-C

Variant names:

• chr6-109295217-T-C
• rs9374080
• ENST00000429614.7:n.301-310T>C

Variant summary

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

The ENST00000429614.7(ENSG00000293541):​n.301-310T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 152,054 control chromosomes in the GnomAD database, including 12,296 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 0.39 (12296 hom., cov: 32)
• Consequence: ENSG00000293541 ENST00000429614.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.33
• Publications: 36 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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC162P	NR_152435.1	n.3863-310T>C		intron_variant	Intron 27 of 45

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293541	ENST00000429614.7	n.301-310T>C		intron_variant	Intron 1 of 3	1
CCDC162P	ENST00000368966.10	n.3895-310T>C		intron_variant	Intron 27 of 45	6
ENSG00000293541	ENST00000422819.6	n.304-310T>C		intron_variant	Intron 1 of 4	2

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59721 AN: 151936 Hom.: 12293 Cov.: 32

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.393 AC: 59733 AN: 152054 Hom.: 12296 Cov.: 32 AF XY: 0.389 AC XY: 28915 AN XY: 74322

African (AFR) AF: 0.352 AC: 14597 AN: 41464

American (AMR) AF: 0.312 AC: 4763 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.436 AC: 1513 AN: 3468

East Asian (EAS) AF: 0.121 AC: 628 AN: 5180

South Asian (SAS) AF: 0.216 AC: 1042 AN: 4820

European-Finnish (FIN) AF: 0.515 AC: 5433 AN: 10558

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.449 AC: 30512 AN: 67962

Other (OTH) AF: 0.387 AC: 818 AN: 2112

Alfa AF: 0.417 Hom.: 39903

Bravo AF: 0.378

Asia WGS AF: 0.191 AC: 666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.6
DANN	Benign	0.70
PhyloP100		2.3

Splicing

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

Other links and lift over

dbSNP: rs9374080; hg19: chr6-109616420;