14-99557059-C-T

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001144995.2(CCDC85C):​c.794-20971G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC85C	NM_001144995.2	c.794-20971G>A		intron_variant	Intron 1 of 5	ENST00000380243.9	NP_001138467.1
CCDC85C	XM_011536706.3	c.794-20971G>A		intron_variant	Intron 1 of 3		XP_011535008.1
CCDC85C	XM_047431328.1	c.794-20971G>A		intron_variant	Intron 1 of 2		XP_047287284.1
CCDC85C	XM_011536707.3	c.794-20971G>A		intron_variant	Intron 1 of 3		XP_011535009.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC85C	ENST00000380243.9	c.794-20971G>A		intron_variant	Intron 1 of 5	5	NM_001144995.2	ENSP00000369592.4
CCDC85C	ENST00000554996.5	c.107-20971G>A		intron_variant	Intron 1 of 5	4		ENSP00000451294.1
CCDC85C	ENST00000556348.1	c.49+15661G>A		intron_variant	Intron 1 of 4	5		ENSP00000451718.1
CCDC85C	ENST00000554877.1	c.-273+19404G>A		intron_variant	Intron 1 of 5	4		ENSP00000452300.1

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.5
DANN	Benign	0.86
PhyloP100		-1.9

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;