chr10-102228229-G-A

Position:

• chr10-102228229-G-A

Variant summary

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

The NM_152310.3(ELOVL3):​c.234-188G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.578 in 151,892 control chromosomes in the GnomAD database, including 26,849 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 0.58 (26849 hom., cov: 31)
• Consequence: ELOVL3 NM_152310.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480

Genes affected

ELOVL3 (HGNC:18047): (ELOVL fatty acid elongase 3) This gene encodes a protein that belongs to the GNS1/SUR4 family. Members of this family play a role in elongation of long chain fatty acids to provide precursors for synthesis of sphingolipids and ceramides. [provided by RefSeq, Jul 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.782 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELOVL3	NM_152310.3	c.234-188G>A		intron_variant		ENST00000370005.4
ELOVL3	XM_011540245.2	c.234-188G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELOVL3	ENST00000370005.4	c.234-188G>A		intron_variant		1	NM_152310.3	P1

Frequencies

GnomAD3 genomes AF: 0.578 AC: 87697 AN: 151774 Hom.: 26786 Cov.: 31

Gnomad AFR AF: 0.789

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.643

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.578 AC: 87817 AN: 151892 Hom.: 26849 Cov.: 31 AF XY: 0.573 AC XY: 42551 AN XY: 74216

Gnomad4 AFR AF: 0.789

Gnomad4 AMR AF: 0.529

Gnomad4 ASJ AF: 0.492

Gnomad4 EAS AF: 0.643

Gnomad4 SAS AF: 0.486

Gnomad4 FIN AF: 0.460

Gnomad4 NFE AF: 0.486

Gnomad4 OTH AF: 0.544

Alfa AF: 0.494 Hom.: 30718

Bravo AF: 0.592

Asia WGS AF: 0.586 AC: 2038 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.3
DANN	Benign	0.38

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: rs10748816; hg19: chr10-103987986;