ENST00000556361.1:n.64+82189A>T

Variant names:

• chr14-66414073-T-A
• rs716234
• ENST00000556361.1:n.64+82189A>T

Variant summary

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

The ENST00000556361.1(ENSG00000258561):​n.64+82189A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 151,788 control chromosomes in the GnomAD database, including 11,870 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 0.32 (11870 hom., cov: 32)
• Consequence: ENSG00000258561 ENST00000556361.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.959

Genes affected

ENSG00000258561 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.649 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+82189A>T		intron_variant	Intron 1 of 3	3
ENSG00000258561	ENST00000556874.1	n.643+82125A>T		intron_variant	Intron 4 of 4	2
CCDC196	ENST00000641761.1	n.874+807T>A		intron_variant	Intron 2 of 9
ENSG00000258561	ENST00000654014.1	n.369+80663A>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.323 AC: 48970 AN: 151670 Hom.: 11838 Cov.: 32

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.323 AC: 49064 AN: 151788 Hom.: 11870 Cov.: 32 AF XY: 0.325 AC XY: 24080 AN XY: 74170

Gnomad4 AFR AF: 0.656

Gnomad4 AMR AF: 0.375

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.466

Gnomad4 SAS AF: 0.324

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.304

Alfa AF: 0.0999 Hom.: 207

Bravo AF: 0.358

Asia WGS AF: 0.373 AC: 1298 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	2.7
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs716234; hg19: chr14-66880791;