chr14-66413944-C-T

Position:

• chr14-66413944-C-T

Variant summary

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

The ENST00000556361.1(ENSG00000258561):​n.64+82318G>A 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 0.337 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: ENST00000556361.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.548

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=-0.87).
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000556361.1	n.64+82318G>A		intron_variant, non_coding_transcript_variant		3
	ENST00000556874.1	n.643+82254G>A		intron_variant, non_coding_transcript_variant		2
CCDC196	ENST00000641761.1	n.874+678C>T		intron_variant, non_coding_transcript_variant
	ENST00000654014.1	n.369+80792G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.664

Gnomad4 AMR AF: 0.388

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.467

Gnomad4 SAS AF: 0.330

Gnomad4 FIN AF: 0.151

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.324

Alfa AF: 0.253 Hom.: 1212

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9332388; hg19: chr14-66880662;