4-110105771-C-T

Variant names:

• chr4-110105771-C-T
• rs10011926
• NM_024090.3:c.90-143G>A

Variant summary

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

The NM_024090.3(ELOVL6):​c.90-143G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 697,072 control chromosomes in the GnomAD database, including 32,429 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 0.31 (8436 hom., cov: 32)
  • Exomes 𝑓: 0.27 (23993 hom.)
• Consequence: ELOVL6 NM_024090.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110
• Publications: 11 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024090.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELOVL6	NM_024090.3	MANE Select	c.90-143G>A		intron	N/A	NP_076995.1
	ELOVL6	NM_001130721.2		c.90-143G>A		intron	N/A	NP_001124193.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELOVL6	ENST00000302274.8	TSL:2 MANE Select	c.90-143G>A		intron	N/A	ENSP00000304736.3
	ELOVL6	ENST00000394607.7	TSL:1	c.90-143G>A		intron	N/A	ENSP00000378105.3
	ELOVL6	ENST00000907637.1		c.90-143G>A		intron	N/A	ENSP00000577696.1

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47127 AN: 151944 Hom.: 8422 Cov.: 32

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.709

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.306

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.281

GnomAD4 exome AF: 0.265 AC: 144539 AN: 545010 Hom.: 23993 AF XY: 0.268 AC XY: 75884 AN XY: 283062

African (AFR) AF: 0.417 AC: 5648 AN: 13550

American (AMR) AF: 0.323 AC: 5863 AN: 18138

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 3345 AN: 13232

East Asian (EAS) AF: 0.711 AC: 20538 AN: 28874

South Asian (SAS) AF: 0.355 AC: 16443 AN: 46322

European-Finnish (FIN) AF: 0.317 AC: 10945 AN: 34526

Middle Eastern (MID) AF: 0.278 AC: 586 AN: 2110

European-Non Finnish (NFE) AF: 0.204 AC: 73561 AN: 360664

Other (OTH) AF: 0.276 AC: 7610 AN: 27594

GnomAD4 genome AF: 0.310 AC: 47185 AN: 152062 Hom.: 8436 Cov.: 32 AF XY: 0.321 AC XY: 23863 AN XY: 74342

African (AFR) AF: 0.413 AC: 17128 AN: 41480

American (AMR) AF: 0.309 AC: 4722 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 864 AN: 3472

East Asian (EAS) AF: 0.709 AC: 3659 AN: 5164

South Asian (SAS) AF: 0.364 AC: 1754 AN: 4824

European-Finnish (FIN) AF: 0.323 AC: 3403 AN: 10548

Middle Eastern (MID) AF: 0.305 AC: 89 AN: 292

European-Non Finnish (NFE) AF: 0.216 AC: 14679 AN: 67976

Other (OTH) AF: 0.281 AC: 594 AN: 2112

Alfa AF: 0.261 Hom.: 17124

Bravo AF: 0.314

Asia WGS AF: 0.500 AC: 1737 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.37
PhyloP100		-0.011
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: rs10011926; hg19: chr4-111026927; COSMIC: COSV56432625;