chr2-56355252-G-C

Variant names:

• chr2-56355252-G-C
• rs7562381
• NM_001080433.2:c.1317+12297G>C

Variant summary

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

The NM_001080433.2(CCDC85A):​c.1317+12297G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 151,988 control chromosomes in the GnomAD database, including 6,323 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 0.26 (6323 hom., cov: 32)
• Consequence: CCDC85A NM_001080433.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.825
• Publications: 1 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC85A	NM_001080433.2	c.1317+12297G>C		intron_variant	Intron 3 of 5	ENST00000407595.3	NP_001073902.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC85A	ENST00000407595.3	c.1317+12297G>C		intron_variant	Intron 3 of 5	1	NM_001080433.2	ENSP00000384040.2
ENSG00000271894	ENST00000607540.2	n.473+12297G>C		intron_variant	Intron 4 of 4	5
ENSG00000271894	ENST00000717261.1	n.348+12297G>C		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39945 AN: 151870 Hom.: 6304 Cov.: 32

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.263 AC: 40020 AN: 151988 Hom.: 6323 Cov.: 32 AF XY: 0.263 AC XY: 19536 AN XY: 74302

African (AFR) AF: 0.438 AC: 18148 AN: 41422

American (AMR) AF: 0.302 AC: 4616 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 494 AN: 3470

East Asian (EAS) AF: 0.145 AC: 751 AN: 5170

South Asian (SAS) AF: 0.155 AC: 748 AN: 4820

European-Finnish (FIN) AF: 0.262 AC: 2759 AN: 10542

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.172 AC: 11691 AN: 67976

Other (OTH) AF: 0.248 AC: 523 AN: 2106

Alfa AF: 0.0990 Hom.: 126

Bravo AF: 0.277

Asia WGS AF: 0.152 AC: 526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.53
DANN	Benign	0.47
PhyloP100		-0.82
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: rs7562381; hg19: chr2-56582387;