rs997154

chr14-22995273-G-A

Variant summary

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

The NM_021944.4(C14orf93):c.918+675C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 152,154 control chromosomes in the GnomAD database, including 3,829 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 0.22 (3829 hom., cov: 31)
• Consequence: C14orf93 NM_021944.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0880

Genes affected

C14orf93 (HGNC:20162): (chromosome 14 open reading frame 93) Enables RNA binding activity. Predicted to act upstream of or within anatomical structure development; cell differentiation; and positive regulation of gene expression. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

AJUBA-DT (HGNC:55449): (AJUBA divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C14orf93	NM_021944.4	c.918+675C>T		intron_variant		ENST00000299088.11
AJUBA-DT	XR_007064074.1	n.956-1901G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C14orf93	ENST00000299088.11	c.918+675C>T		intron_variant		2	NM_021944.4	P1
AJUBA-DT	ENST00000556503.5	n.680-3683G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33600 AN: 152036 Hom.: 3817 Cov.: 31

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.0467

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.221 AC: 33637 AN: 152154 Hom.: 3829 Cov.: 31 AF XY: 0.220 AC XY: 16335 AN XY: 74370

Gnomad4 AFR AF: 0.232

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.262

Gnomad4 EAS AF: 0.0462

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.228

Gnomad4 OTH AF: 0.225

Alfa AF: 0.225 Hom.: 2169

Bravo AF: 0.215

Asia WGS AF: 0.161 AC: 563 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	1.9
Dann	Benign	0.51

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs997154; hg19: chr14-23464482;