2-56364948-A-G

Variant names:

• chr2-56364948-A-G
• rs17268785
• NM_001080433.2:c.1318-7396A>G

Variant summary

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

The NM_001080433.2(CCDC85A):​c.1318-7396A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 152,094 control chromosomes in the GnomAD database, including 3,214 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 0.20 (3214 hom., cov: 32)
• Consequence: CCDC85A NM_001080433.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.457
• Publications: 20 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.24 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC85A	NM_001080433.2	c.1318-7396A>G		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.1318-7396A>G		intron_variant	Intron 3 of 5	1	NM_001080433.2	ENSP00000384040.2
ENSG00000271894	ENST00000607540.2	n.474-19318A>G		intron_variant	Intron 4 of 4	5
ENSG00000271894	ENST00000717261.1	n.349-7396A>G		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30451 AN: 151976 Hom.: 3209 Cov.: 32

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.200 AC: 30473 AN: 152094 Hom.: 3214 Cov.: 32 AF XY: 0.201 AC XY: 14929 AN XY: 74328

African (AFR) AF: 0.244 AC: 10109 AN: 41478

American (AMR) AF: 0.210 AC: 3217 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 454 AN: 3470

East Asian (EAS) AF: 0.146 AC: 754 AN: 5166

South Asian (SAS) AF: 0.157 AC: 757 AN: 4818

European-Finnish (FIN) AF: 0.266 AC: 2808 AN: 10576

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.172 AC: 11718 AN: 67976

Other (OTH) AF: 0.192 AC: 405 AN: 2112

Alfa AF: 0.176 Hom.: 7755

Bravo AF: 0.198

Asia WGS AF: 0.140 AC: 485 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	0.27
DANN	Benign	0.55
PhyloP100		-0.46
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: rs17268785; hg19: chr2-56592083;