15-84095489-T-G

Position:

• chr15-84095489-T-G

Variant summary

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

The NR_036652.1(EFL1P1):​n.393+5196T>G 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 0.528 in 152,012 control chromosomes in the GnomAD database, including 24,321 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 0.53 (24321 hom., cov: 31)
• Consequence: EFL1P1 NR_036652.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37

Genes affected

(HGNC:):

EFL1P1 (HGNC:31739): (elongation factor like GTPase 1 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EFL1P1	NR_036652.1	n.393+5196T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000558550.2	n.333+5196T>G		intron_variant, non_coding_transcript_variant		3
EFL1P1	ENST00000560401.5	n.412+5196T>G		intron_variant, non_coding_transcript_variant
	ENST00000558187.5	n.412+5196T>G		intron_variant, non_coding_transcript_variant		4
	ENST00000701714.1	n.312+5196T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.529 AC: 80284 AN: 151894 Hom.: 24322 Cov.: 31

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.710

Gnomad MID AF: 0.650

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.528 AC: 80296 AN: 152012 Hom.: 24321 Cov.: 31 AF XY: 0.524 AC XY: 38954 AN XY: 74312

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.481

Gnomad4 ASJ AF: 0.667

Gnomad4 EAS AF: 0.261

Gnomad4 SAS AF: 0.535

Gnomad4 FIN AF: 0.710

Gnomad4 NFE AF: 0.690

Gnomad4 OTH AF: 0.591

Alfa AF: 0.649 Hom.: 15265

Bravo AF: 0.499

Asia WGS AF: 0.421 AC: 1466 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.20
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7178655; hg19: chr15-84764241;