2-56274686-C-T

Variant names:

• chr2-56274686-C-T
• rs7576924
• NM_001080433.2:c.1241-68193C>T

Variant summary

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

The ENST00000407595.3(CCDC85A):​c.1241-68193C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 152,094 control chromosomes in the GnomAD database, including 4,883 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 0.25 (4883 hom., cov: 32)
• Consequence: CCDC85A ENST00000407595.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147
• 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000407595.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC85A	NM_001080433.2	MANE Select	c.1241-68193C>T		intron	N/A	NP_001073902.1
	CCDC85A	NM_001348512.1		c.1241-68193C>T		intron	N/A	NP_001335441.1
	CCDC85A	NM_001348513.1		c.1241-68193C>T		intron	N/A	NP_001335442.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC85A	ENST00000407595.3	TSL:1 MANE Select	c.1241-68193C>T		intron	N/A	ENSP00000384040.2
	ENSG00000271894	ENST00000607540.2	TSL:5	n.397-68193C>T		intron	N/A
	ENSG00000271894	ENST00000717261.1		n.272-68193C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.250 AC: 38068 AN: 151976 Hom.: 4868 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.251 AC: 38123 AN: 152094 Hom.: 4883 Cov.: 32 AF XY: 0.258 AC XY: 19199 AN XY: 74336

African (AFR) AF: 0.226 AC: 9396 AN: 41484

American (AMR) AF: 0.304 AC: 4647 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 734 AN: 3468

East Asian (EAS) AF: 0.369 AC: 1908 AN: 5166

South Asian (SAS) AF: 0.359 AC: 1728 AN: 4816

European-Finnish (FIN) AF: 0.323 AC: 3420 AN: 10578

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15324 AN: 67980

Other (OTH) AF: 0.250 AC: 529 AN: 2114

Alfa AF: 0.230 Hom.: 13016

Bravo AF: 0.248

Asia WGS AF: 0.341 AC: 1186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.0
DANN	Benign	0.62
PhyloP100		-0.15
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: rs7576924; hg19: chr2-56501821;