2-54809868-G-C

Variant names:

• chr2-54809868-G-C
• rs4671977
• NM_001039753.4:c.198-3364G>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001039753.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EML6	NM_001039753.4	MANE Select	c.198-3364G>C		intron	N/A	NP_001034842.2	Q6ZMW3-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EML6	ENST00000356458.8	TSL:5 MANE Select	c.198-3364G>C		intron	N/A	ENSP00000348842.6	Q6ZMW3-1
	EML6	ENST00000491655.1	TSL:4	n.236-3364G>C		intron	N/A
	EML6	ENST00000673912.1		n.198-3364G>C		intron	N/A	ENSP00000501234.1	A0A669KBD4

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

African (AFR) AF: 0.147 AC: 6087 AN: 41490

American (AMR) AF: 0.295 AC: 4503 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 1498 AN: 3468

East Asian (EAS) AF: 0.364 AC: 1874 AN: 5148

South Asian (SAS) AF: 0.415 AC: 1998 AN: 4810

European-Finnish (FIN) AF: 0.388 AC: 4083 AN: 10526

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.392 AC: 26616 AN: 67958

Other (OTH) AF: 0.357 AC: 755 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.65
DANN	Benign	0.62
PhyloP100		-0.28
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: rs4671977; hg19: chr2-55037005;