14-94000488-C-T

Variant names:

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

Variant summary

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

The NM_001351596.2(CCDC197):​c.188-657C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,012 control chromosomes in the GnomAD database, including 2,977 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 0.15 (2977 hom., 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.55 is higher than 0.05.

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>T		intron	N/A	NP_001338525.1
	CCDC197	NM_001411045.1		c.188-657C>T		intron	N/A	NP_001397974.1
	CCDC197	NR_024182.1		n.469-343C>T		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>T		intron	N/A	ENSP00000490086.1
	CCDC197	ENST00000359253.2	TSL:1	n.188-657C>T		intron	N/A	ENSP00000490490.1
	CCDC197	ENST00000444118.5	TSL:1	n.*39-343C>T		intron	N/A	ENSP00000489802.1

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22826 AN: 151894 Hom.: 2962 Cov.: 31

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.0716

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.0651

Gnomad EAS AF: 0.566

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.0844

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0533

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.151 AC: 22878 AN: 152012 Hom.: 2977 Cov.: 31 AF XY: 0.154 AC XY: 11436 AN XY: 74322

African (AFR) AF: 0.289 AC: 11954 AN: 41414

American (AMR) AF: 0.127 AC: 1938 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0651 AC: 226 AN: 3470

East Asian (EAS) AF: 0.567 AC: 2913 AN: 5140

South Asian (SAS) AF: 0.196 AC: 944 AN: 4810

European-Finnish (FIN) AF: 0.0844 AC: 894 AN: 10592

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0533 AC: 3625 AN: 67996

Other (OTH) AF: 0.137 AC: 289 AN: 2112

Alfa AF: 0.0838 Hom.: 782

Bravo AF: 0.163

Asia WGS AF: 0.363 AC: 1263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.3
DANN	Benign	0.75
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;