14-93994183-A-T

Position:

• chr14-93994183-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001411045.1(CCDC197):​c.-106-3022A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.426 in 152,048 control chromosomes in the GnomAD database, including 14,062 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 0.43 (14062 hom., cov: 32)
• Consequence: CCDC197 NM_001411045.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.376

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]

LOC124903368 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC197	NM_001411045.1	c.-106-3022A>T		intron_variant			NP_001397974.1
LOC124903368	XR_007064314.1	n.190+2065T>A		intron_variant
LOC124903368	XR_007064315.1	n.203+2065T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC197	ENST00000640978.1	c.-106-3022A>T		intron_variant		5		ENSP00000491594.1

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64767 AN: 151930 Hom.: 14041 Cov.: 32

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.426 AC: 64827 AN: 152048 Hom.: 14062 Cov.: 32 AF XY: 0.426 AC XY: 31665 AN XY: 74328

Gnomad4 AFR AF: 0.437

Gnomad4 AMR AF: 0.519

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.376

Gnomad4 SAS AF: 0.430

Gnomad4 FIN AF: 0.379

Gnomad4 NFE AF: 0.413

Gnomad4 OTH AF: 0.441

Alfa AF: 0.413 Hom.: 1697

Bravo AF: 0.435

Asia WGS AF: 0.432 AC: 1503 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11844114; hg19: chr14-94460529;