2-56297199-T-C

Position:

• chr2-56297199-T-C

Variant summary

Our verdict is Benign. Variant got -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

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 -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC85A	NM_001080433.2	c.1241-45680T>C		intron_variant		ENST00000407595.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC85A	ENST00000407595.3	c.1241-45680T>C		intron_variant		1	NM_001080433.2	P1

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

Gnomad4 AFR AF: 0.864

Gnomad4 AMR AF: 0.866

Gnomad4 ASJ AF: 0.849

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.937

Gnomad4 FIN AF: 0.748

Gnomad4 NFE AF: 0.777

Gnomad4 OTH AF: 0.832

Alfa AF: 0.798 Hom.: 67258

Bravo AF: 0.830

Asia WGS AF: 0.963 AC: 3348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	15
DANN	Benign	0.83

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: rs214038; hg19: chr2-56524334;