2-56328702-G-A

Variant names:

• chr2-56328702-G-A
• rs11677428
• NM_001080433.2:c.1241-14177G>A

Variant summary

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

The NM_001080433.2(CCDC85A):​c.1241-14177G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0982 in 152,116 control chromosomes in the GnomAD database, including 933 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 0.098 (933 hom., cov: 31)
• Consequence: CCDC85A NM_001080433.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.182
• Publications: 0 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC85A	NM_001080433.2	c.1241-14177G>A		intron_variant	Intron 2 of 5	ENST00000407595.3	NP_001073902.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC85A	ENST00000407595.3	c.1241-14177G>A		intron_variant	Intron 2 of 5	1	NM_001080433.2	ENSP00000384040.2
ENSG00000271894	ENST00000607540.2	n.397-14177G>A		intron_variant	Intron 3 of 4	5
ENSG00000271894	ENST00000717261.1	n.272-14177G>A		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.0982 AC: 14925 AN: 151998 Hom.: 931 Cov.: 31

Gnomad AFR AF: 0.0673

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.0616

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.0599

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.0921

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

GnomAD4 genome AF: 0.0982 AC: 14935 AN: 152116 Hom.: 933 Cov.: 31 AF XY: 0.0981 AC XY: 7291 AN XY: 74350

African (AFR) AF: 0.0674 AC: 2798 AN: 41512

American (AMR) AF: 0.0614 AC: 939 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 495 AN: 3468

East Asian (EAS) AF: 0.316 AC: 1625 AN: 5144

South Asian (SAS) AF: 0.186 AC: 896 AN: 4818

European-Finnish (FIN) AF: 0.0599 AC: 634 AN: 10586

Middle Eastern (MID) AF: 0.161 AC: 47 AN: 292

European-Non Finnish (NFE) AF: 0.107 AC: 7254 AN: 67986

Other (OTH) AF: 0.0940 AC: 198 AN: 2106

Alfa AF: 0.0949 Hom.: 343

Bravo AF: 0.0974

Asia WGS AF: 0.260 AC: 904 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.74
DANN	Benign	0.64
PhyloP100		-0.18
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: rs11677428; hg19: chr2-56555837;