rs10149388

Variant names:

• chr14-94000488-C-A
• rs10149388
• NM_001351596.2:c.188-657C>A

Your query was ambiguous. Multiple possible variants found:

• chr14-94000488-C-A
• chr14-94000488-C-G
• chr14-94000488-C-T

Variant summary

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

The NM_001351596.2(CCDC197):​c.188-657C>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: 31)
• Consequence: CCDC197 NM_001351596.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.904
• Publications: 1 publications found

Genes affected

CCDC197 (HGNC:19860): (coiled-coil domain containing 197) Predicted to be integral component of membrane. [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=-0.84).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001351596.2. 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
	CCDC197	NM_001351596.2	MANE Select	c.188-657C>A		intron	N/A	NP_001338525.1
	CCDC197	NM_001411045.1		c.188-657C>A		intron	N/A	NP_001397974.1
	CCDC197	NR_024182.1		n.469-343C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC197	ENST00000636493.2	TSL:5 MANE Select	c.188-657C>A		intron	N/A	ENSP00000490086.1
	CCDC197	ENST00000359253.2	TSL:1	n.188-657C>A		intron	N/A	ENSP00000490490.1
	CCDC197	ENST00000444118.5	TSL:1	n.*39-343C>A		intron	N/A	ENSP00000489802.1

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 782

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.0
DANN	Benign	0.80
PhyloP100		0.90

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10149388; hg19: chr14-94466834;