rs930493

chr2-54831061-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.847+1584G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.368 in 152,044 control chromosomes in the GnomAD database, including 14,642 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 0.37 (14642 hom., cov: 32)
• Consequence: EML6 NM_001039753.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95

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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.73 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EML6	NM_001039753.4	c.847+1584G>A		intron_variant		ENST00000356458.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EML6	ENST00000356458.8	c.847+1584G>A		intron_variant		5	NM_001039753.4	P1
EML6	ENST00000673912.1	c.847+1584G>A		intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.368 AC: 55922 AN: 151928 Hom.: 14604 Cov.: 32

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.368 AC: 56020 AN: 152044 Hom.: 14642 Cov.: 32 AF XY: 0.365 AC XY: 27151 AN XY: 74322

Gnomad4 AFR AF: 0.737

Gnomad4 AMR AF: 0.379

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.396

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.336

Alfa AF: 0.228 Hom.: 2692

Bravo AF: 0.402

Asia WGS AF: 0.324 AC: 1129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.020
Dann	Benign	0.44

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: rs930493; hg19: chr2-55058198;