chr6-109185258-A-G

Position:

• chr6-109185258-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.220+1167A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.732 in 152,166 control chromosomes in the GnomAD database, including 41,111 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 0.73 (41111 hom., cov: 32)
• Consequence: CCDC162P NR_152435.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.957

Genes affected

CCDC162P (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.812 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC162P	NR_152435.1	n.220+1167A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC162P	ENST00000368966.10	n.137+1167A>G		intron_variant		6
CCDC162P	ENST00000640755.1	n.220+1167A>G		intron_variant		5
CCDC162P	ENST00000640771.1	n.218+1167A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.732 AC: 111364 AN: 152048 Hom.: 41068 Cov.: 32

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.797

Gnomad ASJ AF: 0.707

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.832

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.743

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

GnomAD4 genome AF: 0.732 AC: 111457 AN: 152166 Hom.: 41111 Cov.: 32 AF XY: 0.732 AC XY: 54456 AN XY: 74358

Gnomad4 AFR AF: 0.804

Gnomad4 AMR AF: 0.797

Gnomad4 ASJ AF: 0.707

Gnomad4 EAS AF: 0.757

Gnomad4 SAS AF: 0.833

Gnomad4 FIN AF: 0.627

Gnomad4 NFE AF: 0.683

Gnomad4 OTH AF: 0.744

Alfa AF: 0.722 Hom.: 6775

Bravo AF: 0.748

Asia WGS AF: 0.795 AC: 2762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.1
DANN	Benign	0.75

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: rs566164; hg19: chr6-109506461;