2-56367352-T-C

Variant names:

• chr2-56367352-T-C
• rs10180182
• NM_001080433.2:c.1318-4992T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001348512.1(CCDC85A):​c.1318-4992T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.876 in 152,142 control chromosomes in the GnomAD database, including 58,484 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 0.88 (58484 hom., cov: 32)
• Consequence: CCDC85A NM_001348512.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.169
• Publications: 6 publications found

Genes affected

CCDC85A (HGNC:29400): (coiled-coil domain containing 85A) Located in adherens junction. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000271894 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001348512.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC85A	NM_001080433.2	MANE Select	c.1318-4992T>C		intron	N/A	NP_001073902.1
	CCDC85A	NM_001348512.1		c.1318-4992T>C		intron	N/A	NP_001335441.1
	CCDC85A	NM_001348513.1		c.1318-8464T>C		intron	N/A	NP_001335442.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC85A	ENST00000407595.3	TSL:1 MANE Select	c.1318-4992T>C		intron	N/A	ENSP00000384040.2
	CCDC85A	ENST00000894231.1		c.1318-4992T>C		intron	N/A	ENSP00000564290.1
	CCDC85A	ENST00000963878.1		c.1318-8464T>C		intron	N/A	ENSP00000633937.1

Frequencies

GnomAD3 genomes AF: 0.876 AC: 133229 AN: 152024 Hom.: 58442 Cov.: 32

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.814

Gnomad AMR AF: 0.823

Gnomad ASJ AF: 0.858

Gnomad EAS AF: 0.959

Gnomad SAS AF: 0.841

Gnomad FIN AF: 0.900

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.879

Gnomad OTH AF: 0.859

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

GnomAD4 genome AF: 0.876 AC: 133324 AN: 152142 Hom.: 58484 Cov.: 32 AF XY: 0.877 AC XY: 65259 AN XY: 74392

African (AFR) AF: 0.883 AC: 36625 AN: 41486

American (AMR) AF: 0.823 AC: 12572 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.858 AC: 2974 AN: 3468

East Asian (EAS) AF: 0.960 AC: 4966 AN: 5172

South Asian (SAS) AF: 0.842 AC: 4063 AN: 4824

European-Finnish (FIN) AF: 0.900 AC: 9544 AN: 10606

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.879 AC: 59785 AN: 67992

Other (OTH) AF: 0.861 AC: 1813 AN: 2106

Alfa AF: 0.870 Hom.: 83012

Bravo AF: 0.868

Asia WGS AF: 0.887 AC: 3085 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.5
DANN	Benign	0.76
PhyloP100		0.17
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: rs10180182; hg19: chr2-56594487;