rs6726292

chr2-54929493-G-Achr2-54929493-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.4004+742G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 152,038 control chromosomes in the GnomAD database, including 8,194 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 0.32 (8194 hom., cov: 33)
• Consequence: EML6 NM_001039753.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.180

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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EML6	NM_001039753.4	c.4004+742G>A		intron_variant		ENST00000356458.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EML6	ENST00000356458.8	c.4004+742G>A		intron_variant		5	NM_001039753.4	P1
EML6	ENST00000673912.1	c.4004+742G>A		intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48761 AN: 151920 Hom.: 8183 Cov.: 33

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.321 AC: 48824 AN: 152038 Hom.: 8194 Cov.: 33 AF XY: 0.322 AC XY: 23961 AN XY: 74330

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.262

Gnomad4 EAS AF: 0.256

Gnomad4 SAS AF: 0.514

Gnomad4 FIN AF: 0.259

Gnomad4 NFE AF: 0.277

Gnomad4 OTH AF: 0.311

Alfa AF: 0.277 Hom.: 9204

Bravo AF: 0.328

Asia WGS AF: 0.402 AC: 1400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.54
Dann	Benign	0.58

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: rs6726292; hg19: chr2-55156630;