NM_018696.3:c.158-1318T>A

Variant names:

• chr18-50982778-T-A
• rs620898
• NM_018696.3:c.158-1318T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018696.3(ELAC1):​c.158-1318T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 151,996 control chromosomes in the GnomAD database, including 21,341 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 0.51 (21341 hom., cov: 32)
• Consequence: ELAC1 NM_018696.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77
• Publications: 5 publications found

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]

ENSG00000267699 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.735 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELAC1	NM_018696.3	c.158-1318T>A		intron_variant	Intron 2 of 3	ENST00000269466.8	NP_061166.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELAC1	ENST00000269466.8	c.158-1318T>A		intron_variant	Intron 2 of 3	1	NM_018696.3	ENSP00000269466.3
ENSG00000267699	ENST00000590722.2	n.157+8217T>A		intron_variant	Intron 2 of 8	2		ENSP00000465737.1

Frequencies

GnomAD3 genomes AF: 0.508 AC: 77156 AN: 151878 Hom.: 21299 Cov.: 32

Gnomad AFR AF: 0.742

Gnomad AMI AF: 0.625

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.417

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.508 AC: 77261 AN: 151996 Hom.: 21341 Cov.: 32 AF XY: 0.505 AC XY: 37556 AN XY: 74304

African (AFR) AF: 0.742 AC: 30771 AN: 41472

American (AMR) AF: 0.453 AC: 6907 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.473 AC: 1643 AN: 3470

East Asian (EAS) AF: 0.543 AC: 2806 AN: 5164

South Asian (SAS) AF: 0.325 AC: 1567 AN: 4818

European-Finnish (FIN) AF: 0.417 AC: 4406 AN: 10558

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.403 AC: 27380 AN: 67940

Other (OTH) AF: 0.506 AC: 1068 AN: 2110

Alfa AF: 0.457 Hom.: 2164

Bravo AF: 0.529

Asia WGS AF: 0.462 AC: 1606 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.029
DANN	Benign	0.76
PhyloP100		-1.8
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs620898; hg19: chr18-48509148;