4-110057342-A-G

Variant names:

• chr4-110057342-A-G
• rs1557803
• NM_024090.3:c.373+2261T>C

Variant summary

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

The NM_024090.3(ELOVL6):​c.373+2261T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.502 in 151,524 control chromosomes in the GnomAD database, including 22,413 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 0.50 (22413 hom., cov: 29)
• Consequence: ELOVL6 NM_024090.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81

Genes affected

ELOVL6 (HGNC:15829): (ELOVL fatty acid elongase 6) Fatty acid elongases (EC 6.2.1.3), such as ELOVL6, use malonyl-CoA as a 2-carbon donor in the first and rate-limiting step of fatty acid elongation (Moon et al., 2001 [PubMed 11567032]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELOVL6	NM_024090.3	c.373+2261T>C		intron_variant	Intron 3 of 3	ENST00000302274.8	NP_076995.1
ELOVL6	NM_001130721.2	c.373+2261T>C		intron_variant	Intron 4 of 4		NP_001124193.1
ELOVL6	XM_011532233.4	c.373+2261T>C		intron_variant	Intron 4 of 4		XP_011530535.1
ELOVL6	XM_011532234.4	c.373+2261T>C		intron_variant	Intron 4 of 4		XP_011530536.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELOVL6	ENST00000302274.8	c.373+2261T>C		intron_variant	Intron 3 of 3	2	NM_024090.3	ENSP00000304736.3

Frequencies

GnomAD3 genomes AF: 0.501 AC: 75909 AN: 151406 Hom.: 22345 Cov.: 29

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.502 AC: 76035 AN: 151524 Hom.: 22413 Cov.: 29 AF XY: 0.509 AC XY: 37641 AN XY: 74014

Gnomad4 AFR AF: 0.800

Gnomad4 AMR AF: 0.567

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.684

Gnomad4 SAS AF: 0.458

Gnomad4 FIN AF: 0.389

Gnomad4 NFE AF: 0.322

Gnomad4 OTH AF: 0.466

Alfa AF: 0.350 Hom.: 13015

Bravo AF: 0.531

Asia WGS AF: 0.637 AC: 2216 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.17
DANN	Benign	0.36

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: rs1557803; hg19: chr4-110978498;