rs1961245

chr2-54866705-G-A

Variant summary

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

The NM_001039753.4(EML6):c.1933-61G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.405 in 845,580 control chromosomes in the GnomAD database, including 73,407 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 0.45 (16240 hom., cov: 32)
  • Exomes 𝑓: 0.40 (57167 hom.)
• Consequence: EML6 NM_001039753.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EML6	NM_001039753.4	c.1933-61G>A		intron_variant		ENST00000356458.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EML6	ENST00000356458.8	c.1933-61G>A		intron_variant		5	NM_001039753.4	P1
EML6	ENST00000673912.1	c.1933-61G>A		intron_variant, NMD_transcript_variant
EML6	ENST00000493997.1	n.281-61G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.448 AC: 68112 AN: 151922 Hom.: 16222 Cov.: 32

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.440

GnomAD4 exome AF: 0.396 AC: 274347 AN: 693540 Hom.: 57167 AF XY: 0.402 AC XY: 144208 AN XY: 358838

Gnomad4 AFR exome AF: 0.614

Gnomad4 AMR exome AF: 0.413

Gnomad4 ASJ exome AF: 0.398

Gnomad4 EAS exome AF: 0.549

Gnomad4 SAS exome AF: 0.559

Gnomad4 FIN exome AF: 0.423

Gnomad4 NFE exome AF: 0.355

Gnomad4 OTH exome AF: 0.411

GnomAD4 genome AF: 0.448 AC: 68181 AN: 152040 Hom.: 16240 Cov.: 32 AF XY: 0.453 AC XY: 33705 AN XY: 74330

Gnomad4 AFR AF: 0.597

Gnomad4 AMR AF: 0.414

Gnomad4 ASJ AF: 0.405

Gnomad4 EAS AF: 0.546

Gnomad4 SAS AF: 0.566

Gnomad4 FIN AF: 0.443

Gnomad4 NFE AF: 0.354

Gnomad4 OTH AF: 0.440

Alfa AF: 0.390 Hom.: 6589

Bravo AF: 0.451

Asia WGS AF: 0.554 AC: 1925 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.16
Dann	Benign	0.19

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: rs1961245; hg19: chr2-55093842; COSMIC: COSV62863362;