rs11677428

Positions:

• chr2-56328702-G-A
• chr2-56328702-G-C

Variant summary

Our verdict is Benign. Variant got -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

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=-0.89).
• 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/exons	MANE	UniProt
CCDC85A	NM_001080433.2	c.1241-14177G>A		intron_variant		ENST00000407595.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC85A	ENST00000407595.3	c.1241-14177G>A		intron_variant		1	NM_001080433.2	P1

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

Gnomad4 AFR AF: 0.0674

Gnomad4 AMR AF: 0.0614

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.316

Gnomad4 SAS AF: 0.186

Gnomad4 FIN AF: 0.0599

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.0940

Alfa AF: 0.104 Hom.: 192

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

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: rs11677428; hg19: chr2-56555837;