rs7767017

Positions:

• chr6-109198719-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_152435.1(CCDC162P):​n.867+207A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 152,052 control chromosomes in the GnomAD database, including 8,479 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 0.27 (8479 hom., cov: 32)
• Consequence: CCDC162P NR_152435.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.102

Genes affected

CCDC162P (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC162P	NR_152435.1	n.867+207A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC162P	ENST00000368966.10	n.784+207A>G		intron_variant		6
CCDC162P	ENST00000640755.1	n.867+207A>G		intron_variant		5
CCDC162P	ENST00000640771.1	n.865+207A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40773 AN: 151934 Hom.: 8461 Cov.: 32

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.0626

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.269 AC: 40835 AN: 152052 Hom.: 8479 Cov.: 32 AF XY: 0.268 AC XY: 19922 AN XY: 74336

Gnomad4 AFR AF: 0.584

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.226

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.232

Alfa AF: 0.162 Hom.: 2501

Bravo AF: 0.278

Asia WGS AF: 0.228 AC: 792 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.54

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7767017; hg19: chr6-109519922;