rs8052123

Positions:

• chr16-57529759-T-C

Variant summary

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

The NM_033212.4(CCDC102A):​c.-147-435A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 152,112 control chromosomes in the GnomAD database, including 2,577 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 0.17 (2577 hom., cov: 32)
• Consequence: CCDC102A NM_033212.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.406

Genes affected

CCDC102A (HGNC:28097): (coiled-coil domain containing 102A) Predicted to be part of myosin complex. [provided by Alliance of Genome Resources, Apr 2022]

ADGRG5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC102A	NM_033212.4	c.-147-435A>G		intron_variant		ENST00000258214.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC102A	ENST00000258214.3	c.-147-435A>G		intron_variant		1	NM_033212.4	P1

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25435 AN: 151994 Hom.: 2551 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.168 AC: 25506 AN: 152112 Hom.: 2577 Cov.: 32 AF XY: 0.168 AC XY: 12493 AN XY: 74354

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.150

Alfa AF: 0.118 Hom.: 1914

Bravo AF: 0.174

Asia WGS AF: 0.221 AC: 768 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.5
DANN	Benign	0.78

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: rs8052123; hg19: chr16-57563671;