2-56367352-T-C

Position:

• chr2-56367352-T-C

Variant summary

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

The NM_001080433.2(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_001080433.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.169

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC85A	NM_001080433.2	c.1318-4992T>C		intron_variant		ENST00000407595.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC85A	ENST00000407595.3	c.1318-4992T>C		intron_variant		1	NM_001080433.2	P1

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

Gnomad4 AFR AF: 0.883

Gnomad4 AMR AF: 0.823

Gnomad4 ASJ AF: 0.858

Gnomad4 EAS AF: 0.960

Gnomad4 SAS AF: 0.842

Gnomad4 FIN AF: 0.900

Gnomad4 NFE AF: 0.879

Gnomad4 OTH AF: 0.861

Alfa AF: 0.871 Hom.: 56541

Bravo AF: 0.868

Asia WGS AF: 0.887 AC: 3085 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.5
DANN	Benign	0.76

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: rs10180182; hg19: chr2-56594487;