chr5-60833534-A-G

Variant names:

• chr5-60833534-A-G
• rs6869332
• NM_024930.3:c.-86+10626T>C

Variant summary

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

The ENST00000508821.6(ELOVL7):​c.-86+10626T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.811 in 152,004 control chromosomes in the GnomAD database, including 50,158 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 0.81 (50158 hom., cov: 30)
• Consequence: ELOVL7 ENST00000508821.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.176
• Publications: 7 publications found

Genes affected

ELOVL7 (HGNC:26292): (ELOVL fatty acid elongase 7) Enables fatty acid elongase activity. Involved in fatty acid elongation, polyunsaturated fatty acid; fatty acid elongation, saturated fatty acid; and very long-chain fatty acid biosynthetic process. Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000508821.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELOVL7	NM_024930.3	MANE Select	c.-86+10626T>C		intron	N/A	NP_079206.2
	ELOVL7	NM_001104558.2		c.-35+10626T>C		intron	N/A	NP_001098028.1
	ELOVL7	NM_001297617.2		c.-472+10626T>C		intron	N/A	NP_001284546.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELOVL7	ENST00000508821.6	TSL:1 MANE Select	c.-86+10626T>C		intron	N/A	ENSP00000424123.1
	ELOVL7	ENST00000505959.5	TSL:1	c.-472+10626T>C		intron	N/A	ENSP00000421043.1
	ELOVL7	ENST00000425382.5	TSL:5	c.-35+10626T>C		intron	N/A	ENSP00000402634.1

Frequencies

GnomAD3 genomes AF: 0.811 AC: 123125 AN: 151886 Hom.: 50124 Cov.: 30

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.750

Gnomad ASJ AF: 0.843

Gnomad EAS AF: 0.903

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.816

Gnomad OTH AF: 0.819

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

GnomAD4 genome AF: 0.811 AC: 123208 AN: 152004 Hom.: 50158 Cov.: 30 AF XY: 0.808 AC XY: 60031 AN XY: 74296

African (AFR) AF: 0.822 AC: 34069 AN: 41422

American (AMR) AF: 0.750 AC: 11470 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.843 AC: 2924 AN: 3470

East Asian (EAS) AF: 0.904 AC: 4671 AN: 5168

South Asian (SAS) AF: 0.715 AC: 3429 AN: 4798

European-Finnish (FIN) AF: 0.805 AC: 8507 AN: 10562

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.816 AC: 55490 AN: 67984

Other (OTH) AF: 0.813 AC: 1715 AN: 2110

Alfa AF: 0.806 Hom.: 27548

Bravo AF: 0.811

Asia WGS AF: 0.784 AC: 2728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.0
DANN	Benign	0.76
PhyloP100		0.18
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs6869332; hg19: chr5-60129361;