2-54809868-G-C

Position:

• chr2-54809868-G-C

Variant summary

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

The NM_001039753.4(EML6):​c.198-3364G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 151,988 control chromosomes in the GnomAD database, including 8,478 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 (8478 hom., cov: 32)
• Consequence: EML6 NM_001039753.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.281

Genes affected

EML6 (HGNC:35412): (EMAP like 6) Predicted to enable microtubule binding activity. Predicted to be located in cytoplasm and microtubule. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EML6	NM_001039753.4	c.198-3364G>C		intron_variant		ENST00000356458.8	NP_001034842.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EML6	ENST00000356458.8	c.198-3364G>C		intron_variant		5	NM_001039753.4	ENSP00000348842	P1
EML6	ENST00000673912.1	c.198-3364G>C		intron_variant, NMD_transcript_variant				ENSP00000501234
EML6	ENST00000491655.1	n.236-3364G>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47820 AN: 151870 Hom.: 8476 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.315 AC: 47828 AN: 151988 Hom.: 8478 Cov.: 32 AF XY: 0.319 AC XY: 23675 AN XY: 74256

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.432

Gnomad4 EAS AF: 0.364

Gnomad4 SAS AF: 0.415

Gnomad4 FIN AF: 0.388

Gnomad4 NFE AF: 0.392

Gnomad4 OTH AF: 0.357

Alfa AF: 0.222 Hom.: 542

Bravo AF: 0.297

Asia WGS AF: 0.399 AC: 1386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.65
DANN	Benign	0.62

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: rs4671977; hg19: chr2-55037005;