rs716234

chr14-66414073-T-Achr14-66414073-T-C

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, non coding transcript 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: ENST00000556361.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.959

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000556361.1	n.64+82189A>T		intron_variant, non_coding_transcript_variant		3
	ENST00000556874.1	n.643+82125A>T		intron_variant, non_coding_transcript_variant		2
CCDC196	ENST00000641761.1	n.874+807T>A		intron_variant, non_coding_transcript_variant
	ENST00000654014.1	n.369+80663A>T		intron_variant, non_coding_transcript_variant

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;