chr4-110048926-C-G

Variant names:

• chr4-110048926-C-G
• rs17041272
• NM_024090.3:c.*2412G>C

Variant summary

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

The NM_024090.3(ELOVL6):​c.*2412G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0954 in 152,136 control chromosomes in the GnomAD database, including 985 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 0.095 (985 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ELOVL6 NM_024090.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229

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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELOVL6	NM_024090.3	c.*2412G>C		3_prime_UTR_variant	Exon 4 of 4	ENST00000302274.8	NP_076995.1
ELOVL6	NM_001130721.2	c.*2412G>C		3_prime_UTR_variant	Exon 5 of 5		NP_001124193.1
ELOVL6	XM_011532233.4	c.*2412G>C		3_prime_UTR_variant	Exon 5 of 5		XP_011530535.1
ELOVL6	XM_011532234.4	c.*2412G>C		3_prime_UTR_variant	Exon 5 of 5		XP_011530536.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELOVL6	ENST00000302274	c.*2412G>C		3_prime_UTR_variant	Exon 4 of 4	2	NM_024090.3	ENSP00000304736.3
ELOVL6	ENST00000394607	c.*2412G>C		3_prime_UTR_variant	Exon 5 of 5	1		ENSP00000378105.3

Frequencies

GnomAD3 genomes AF: 0.0953 AC: 14485 AN: 152018 Hom.: 986 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.199

Gnomad AMR AF: 0.0862

Gnomad ASJ AF: 0.0654

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.0856

Gnomad FIN AF: 0.0970

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0459

Gnomad OTH AF: 0.0806

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.0954 AC: 14508 AN: 152136 Hom.: 985 Cov.: 32 AF XY: 0.0982 AC XY: 7301 AN XY: 74364

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.0861

Gnomad4 ASJ AF: 0.0654

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.0859

Gnomad4 FIN AF: 0.0970

Gnomad4 NFE AF: 0.0459

Gnomad4 OTH AF: 0.0826

Alfa AF: 0.0332 Hom.: 27

Bravo AF: 0.0973

Asia WGS AF: 0.145 AC: 506 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.4
DANN	Benign	0.37

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: rs17041272; hg19: chr4-110970082;