NM_017770.4:c.3+5950A>C

Variant names:

• chr6-11038278-T-G
• rs7744440
• NM_017770.4:c.3+5950A>C

Variant summary

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

The NM_017770.4(ELOVL2):​c.3+5950A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 152,054 control chromosomes in the GnomAD database, including 14,527 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 0.38 (14527 hom., cov: 32)
• Consequence: ELOVL2 NM_017770.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126
• Publications: 8 publications found

Genes affected

ELOVL2 (HGNC:14416): (ELOVL fatty acid elongase 2) Enables fatty acid elongase activity. Involved in fatty acid elongation, polyunsaturated 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 (AFR) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017770.4. 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
	ELOVL2	NM_017770.4	MANE Select	c.3+5950A>C		intron	N/A	NP_060240.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELOVL2	ENST00000354666.4	TSL:1 MANE Select	c.3+5950A>C		intron	N/A	ENSP00000346693.3

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58153 AN: 151936 Hom.: 14478 Cov.: 32

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.383 AC: 58260 AN: 152054 Hom.: 14527 Cov.: 32 AF XY: 0.374 AC XY: 27775 AN XY: 74336

African (AFR) AF: 0.710 AC: 29425 AN: 41422

American (AMR) AF: 0.353 AC: 5386 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1327 AN: 3470

East Asian (EAS) AF: 0.269 AC: 1392 AN: 5178

South Asian (SAS) AF: 0.270 AC: 1300 AN: 4814

European-Finnish (FIN) AF: 0.119 AC: 1259 AN: 10586

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.250 AC: 16974 AN: 67994

Other (OTH) AF: 0.406 AC: 858 AN: 2114

Alfa AF: 0.349 Hom.: 6886

Bravo AF: 0.414

Asia WGS AF: 0.317 AC: 1105 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
DANN	Benign	0.47
PhyloP100		-0.13
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: rs7744440; hg19: chr6-11038511;