rs10516560

Variant names:

• chr4-110133239-G-C
• rs10516560
• NM_024090.3:c.90-27611C>G

Variant summary

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

The NM_024090.3(ELOVL6):​c.90-27611C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0157 in 152,246 control chromosomes in the GnomAD database, including 54 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 0.016 (54 hom., cov: 32)
• Consequence: ELOVL6 NM_024090.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.377
• Publications: 2 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0891 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELOVL6	NM_024090.3	c.90-27611C>G		intron_variant	Intron 1 of 3	ENST00000302274.8	NP_076995.1
ELOVL6	NM_001130721.2	c.90-27611C>G		intron_variant	Intron 2 of 4		NP_001124193.1
ELOVL6	XM_011532233.4	c.90-27611C>G		intron_variant	Intron 2 of 4		XP_011530535.1
ELOVL6	XM_011532234.4	c.90-27611C>G		intron_variant	Intron 2 of 4		XP_011530536.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELOVL6	ENST00000302274.8	c.90-27611C>G		intron_variant	Intron 1 of 3	2	NM_024090.3	ENSP00000304736.3

Frequencies

GnomAD3 genomes AF: 0.0157 AC: 2381 AN: 152128 Hom.: 52 Cov.: 32

Gnomad AFR AF: 0.00519

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0145

Gnomad ASJ AF: 0.0170

Gnomad EAS AF: 0.0844

Gnomad SAS AF: 0.0968

Gnomad FIN AF: 0.0155

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0115

Gnomad OTH AF: 0.0144

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

GnomAD4 genome AF: 0.0157 AC: 2395 AN: 152246 Hom.: 54 Cov.: 32 AF XY: 0.0174 AC XY: 1292 AN XY: 74436

African (AFR) AF: 0.00517 AC: 215 AN: 41546

American (AMR) AF: 0.0151 AC: 231 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0170 AC: 59 AN: 3468

East Asian (EAS) AF: 0.0848 AC: 439 AN: 5178

South Asian (SAS) AF: 0.0963 AC: 464 AN: 4818

European-Finnish (FIN) AF: 0.0155 AC: 165 AN: 10612

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0115 AC: 784 AN: 68014

Other (OTH) AF: 0.0175 AC: 37 AN: 2112

Alfa AF: 0.00985 Hom.: 1

Bravo AF: 0.0143

Asia WGS AF: 0.0920 AC: 317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.7
DANN	Benign	0.50
PhyloP100		0.38
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: rs10516560; hg19: chr4-111054395;