rs9332388

Variant names:

• chr14-66413944-C-T
• rs9332388
• ENST00000556361.1:n.64+82318G>A

Variant summary

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

The ENST00000556361.1(ENSG00000258561):​n.64+82318G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 151,882 control chromosomes in the GnomAD database, including 12,449 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 0.34 (12449 hom., cov: 32)
• Consequence: ENSG00000258561 ENST00000556361.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.548
• Publications: 1 publications found

Genes affected

ENSG00000258561 (HGNC:):

CCDC196 (HGNC:20100): (coiled-coil domain containing 196)

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 (AFR) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000258561	ENST00000556361.1	n.64+82318G>A		intron_variant	Intron 1 of 3	3
ENSG00000258561	ENST00000556874.1	n.643+82254G>A		intron_variant	Intron 4 of 4	2
CCDC196	ENST00000641761.1	n.874+678C>T		intron_variant	Intron 2 of 9
ENSG00000258561	ENST00000654014.1	n.369+80792G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51113 AN: 151764 Hom.: 12406 Cov.: 32

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.337 AC: 51226 AN: 151882 Hom.: 12449 Cov.: 32 AF XY: 0.339 AC XY: 25172 AN XY: 74252

African (AFR) AF: 0.664 AC: 27542 AN: 41452

American (AMR) AF: 0.388 AC: 5911 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 817 AN: 3468

East Asian (EAS) AF: 0.467 AC: 2387 AN: 5108

South Asian (SAS) AF: 0.330 AC: 1590 AN: 4812

European-Finnish (FIN) AF: 0.151 AC: 1602 AN: 10602

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10398 AN: 67914

Other (OTH) AF: 0.324 AC: 681 AN: 2104

Alfa AF: 0.266 Hom.: 1385

Bravo AF: 0.371

Asia WGS AF: 0.405 AC: 1407 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.5
DANN	Benign	0.34
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs9332388; hg19: chr14-66880662;