6-109313625-A-G

Position:

• chr6-109313625-A-G

Variant summary

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

The ENST00000508210.1(CCDC162P):​n.386-438A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 152,160 control chromosomes in the GnomAD database, including 5,923 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 0.26 (5923 hom., cov: 32)
• Consequence: CCDC162P ENST00000508210.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.151

Genes affected

CCDC162P (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC162P	NR_152435.1	n.4571-438A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC162P	ENST00000368966.10	n.4603-438A>G		intron_variant		6
CCDC162P	ENST00000506861.1	n.348+3971A>G		intron_variant		4
CCDC162P	ENST00000508210.1	n.386-438A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.258 AC: 39168 AN: 152042 Hom.: 5922 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.257 AC: 39174 AN: 152160 Hom.: 5923 Cov.: 32 AF XY: 0.257 AC XY: 19152 AN XY: 74380

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.277

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.411

Gnomad4 NFE AF: 0.342

Gnomad4 OTH AF: 0.260

Alfa AF: 0.311 Hom.: 17631

Bravo AF: 0.238

Asia WGS AF: 0.137 AC: 478 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	3.7
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11966072; hg19: chr6-109634828;