18-50979044-C-T

Position:

• chr18-50979044-C-T

Variant summary

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

The NM_018696.3(ELAC1):​c.157+4483C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 152,060 control chromosomes in the GnomAD database, including 10,679 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 0.37 (10679 hom., cov: 32)
• Consequence: ELAC1 NM_018696.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200

Genes affected

ELAC1 (HGNC:14197): (elaC ribonuclease Z 1) Predicted to enable 3'-tRNA processing endoribonuclease activity. Predicted to be involved in tRNA 3'-trailer cleavage, endonucleolytic. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

LOC107985152 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELAC1	NM_018696.3	c.157+4483C>T		intron_variant		ENST00000269466.8
LOC107985152	XR_007066371.1	n.10777-4051G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELAC1	ENST00000269466.8	c.157+4483C>T		intron_variant		1	NM_018696.3	P1
ELAC1	ENST00000591429.1	c.157+4483C>T		intron_variant		1
ELAC1	ENST00000588577.5	c.157+4483C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.372 AC: 56534 AN: 151942 Hom.: 10678 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.372 AC: 56571 AN: 152060 Hom.: 10679 Cov.: 32 AF XY: 0.370 AC XY: 27528 AN XY: 74338

Gnomad4 AFR AF: 0.346

Gnomad4 AMR AF: 0.380

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.451

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.379

Gnomad4 OTH AF: 0.386

Alfa AF: 0.382 Hom.: 11015

Bravo AF: 0.377

Asia WGS AF: 0.358 AC: 1244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.6
DANN	Benign	0.66

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: rs2027735; hg19: chr18-48505414;