NM_001144995.2:c.794-20971G>T

Variant names:

• chr14-99557059-C-A
• rs4445835
• NM_001144995.2:c.794-20971G>T

Variant summary

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

The NM_001144995.2(CCDC85C):​c.794-20971G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.538 in 152,076 control chromosomes in the GnomAD database, including 22,268 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 0.54 (22268 hom., cov: 33)
• Consequence: CCDC85C NM_001144995.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86
• Publications: 4 publications found

Genes affected

CCDC85C (HGNC:35459): (coiled-coil domain containing 85C) Predicted to be involved in cerebral cortex development. Located in adherens junction. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001144995.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC85C	NM_001144995.2	MANE Select	c.794-20971G>T		intron	N/A	NP_001138467.1	A6NKD9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC85C	ENST00000380243.9	TSL:5 MANE Select	c.794-20971G>T		intron	N/A	ENSP00000369592.4	A6NKD9
	CCDC85C	ENST00000554996.5	TSL:4	c.107-20971G>T		intron	N/A	ENSP00000451294.1	H0YJE0
	CCDC85C	ENST00000556348.1	TSL:5	c.49+15661G>T		intron	N/A	ENSP00000451718.1	G3V4C8

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81735 AN: 151956 Hom.: 22234 Cov.: 33

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.573

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.538 AC: 81825 AN: 152076 Hom.: 22268 Cov.: 33 AF XY: 0.533 AC XY: 39662 AN XY: 74346

African (AFR) AF: 0.608 AC: 25181 AN: 41448

American (AMR) AF: 0.573 AC: 8768 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.521 AC: 1808 AN: 3472

East Asian (EAS) AF: 0.559 AC: 2883 AN: 5160

South Asian (SAS) AF: 0.572 AC: 2755 AN: 4818

European-Finnish (FIN) AF: 0.415 AC: 4388 AN: 10574

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.507 AC: 34468 AN: 67998

Other (OTH) AF: 0.526 AC: 1109 AN: 2110

Alfa AF: 0.476 Hom.: 3775

Bravo AF: 0.554

Asia WGS AF: 0.547 AC: 1904 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.7
DANN	Benign	0.85
PhyloP100		-1.9
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: rs4445835; hg19: chr14-100023396;