rs1159916

chr2-56232093-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.1240+38653T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 151,882 control chromosomes in the GnomAD database, including 6,651 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 0.29 (6651 hom., cov: 31)
• Consequence: CCDC85A NM_001080433.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

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=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC85A	NM_001080433.2	c.1240+38653T>C		intron_variant		ENST00000407595.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC85A	ENST00000407595.3	c.1240+38653T>C		intron_variant		1	NM_001080433.2	P1

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44574 AN: 151766 Hom.: 6647 Cov.: 31

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.350

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.294 AC: 44596 AN: 151882 Hom.: 6651 Cov.: 31 AF XY: 0.293 AC XY: 21755 AN XY: 74224

Gnomad4 AFR AF: 0.273

Gnomad4 AMR AF: 0.356

Gnomad4 ASJ AF: 0.469

Gnomad4 EAS AF: 0.230

Gnomad4 SAS AF: 0.242

Gnomad4 FIN AF: 0.277

Gnomad4 NFE AF: 0.295

Gnomad4 OTH AF: 0.319

Alfa AF: 0.310 Hom.: 1903

Bravo AF: 0.301

Asia WGS AF: 0.257 AC: 892 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	5.5
Dann	Benign	0.84

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: rs1159916; hg19: chr2-56459228;