2-56297199-T-C

Variant names:

• chr2-56297199-T-C
• rs214038
• NM_001080433.2:c.1241-45680T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001080433.2(CCDC85A):​c.1241-45680T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.823 in 152,030 control chromosomes in the GnomAD database, including 51,714 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 0.82 (51714 hom., cov: 30)
• Consequence: CCDC85A NM_001080433.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.497
• Publications: 4 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001080433.2. 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
	CCDC85A	NM_001080433.2	MANE Select	c.1241-45680T>C		intron	N/A	NP_001073902.1	Q96PX6
	CCDC85A	NM_001348512.1		c.1241-45680T>C		intron	N/A	NP_001335441.1
	CCDC85A	NM_001348513.1		c.1241-45680T>C		intron	N/A	NP_001335442.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC85A	ENST00000407595.3	TSL:1 MANE Select	c.1241-45680T>C		intron	N/A	ENSP00000384040.2	Q96PX6
	CCDC85A	ENST00000894231.1		c.1241-45680T>C		intron	N/A	ENSP00000564290.1
	CCDC85A	ENST00000963878.1		c.1241-45680T>C		intron	N/A	ENSP00000633937.1

Frequencies

GnomAD3 genomes AF: 0.822 AC: 124940 AN: 151912 Hom.: 51654 Cov.: 30

Gnomad AFR AF: 0.863

Gnomad AMI AF: 0.769

Gnomad AMR AF: 0.866

Gnomad ASJ AF: 0.849

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.937

Gnomad FIN AF: 0.748

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.777

Gnomad OTH AF: 0.831

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

GnomAD4 genome AF: 0.823 AC: 125058 AN: 152030 Hom.: 51714 Cov.: 30 AF XY: 0.824 AC XY: 61233 AN XY: 74306

African (AFR) AF: 0.864 AC: 35815 AN: 41470

American (AMR) AF: 0.866 AC: 13204 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.849 AC: 2946 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5149 AN: 5158

South Asian (SAS) AF: 0.937 AC: 4521 AN: 4824

European-Finnish (FIN) AF: 0.748 AC: 7899 AN: 10562

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.777 AC: 52811 AN: 67984

Other (OTH) AF: 0.832 AC: 1758 AN: 2112

Alfa AF: 0.806 Hom.: 106614

Bravo AF: 0.830

Asia WGS AF: 0.963 AC: 3348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	15
DANN	Benign	0.83
PhyloP100		0.50
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: rs214038; hg19: chr2-56524334;