chr16-57529759-T-C

Variant names:

• chr16-57529759-T-C
• rs8052123
• NM_033212.4:c.-147-435A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

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:19010): (adhesion G protein-coupled receptor G5) This gene encodes a member of the adhesion family of G-protein coupled receptors. Members of this family are characterized by long N-termini and multiple functional domains. They may play a role in the immune system as well as in the central nervous system. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_033212.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC102A	NM_033212.4	MANE Select	c.-147-435A>G		intron	N/A	NP_149989.2	Q96A19

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC102A	ENST00000258214.3	TSL:1 MANE Select	c.-147-435A>G		intron	N/A	ENSP00000258214.2	Q96A19
	CCDC102A	ENST00000870632.1		c.-147-435A>G		intron	N/A	ENSP00000540691.1
	CCDC102A	ENST00000870633.1		c.-147-435A>G		intron	N/A	ENSP00000540692.1

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

African (AFR) AF: 0.287 AC: 11891 AN: 41464

American (AMR) AF: 0.138 AC: 2113 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 377 AN: 3470

East Asian (EAS) AF: 0.204 AC: 1053 AN: 5160

South Asian (SAS) AF: 0.142 AC: 683 AN: 4822

European-Finnish (FIN) AF: 0.126 AC: 1335 AN: 10594

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7516 AN: 67988

Other (OTH) AF: 0.150 AC: 317 AN: 2108

Alfa AF: 0.128 Hom.: 5827

Bravo AF: 0.174

Asia WGS AF: 0.221 AC: 768 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.5
DANN	Benign	0.78
PhyloP100		-0.41
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs8052123; hg19: chr16-57563671;