chr2-54914852-T-C

Variant names:

• chr2-54914852-T-C
• rs4671993
• NM_001039753.4:c.3499-1907T>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.3499-1907T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0711 in 152,224 control chromosomes in the GnomAD database, including 665 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 0.071 (665 hom., cov: 32)
• Consequence: EML6 NM_001039753.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.825
• Publications: 2 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=-0.67).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EML6	NM_001039753.4	c.3499-1907T>C		intron_variant	Intron 25 of 41	ENST00000356458.8	NP_001034842.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EML6	ENST00000356458.8	c.3499-1907T>C		intron_variant	Intron 25 of 41	5	NM_001039753.4	ENSP00000348842.6
EML6	ENST00000673912.1	n.3499-1907T>C		intron_variant	Intron 25 of 42			ENSP00000501234.1

Frequencies

GnomAD3 genomes AF: 0.0710 AC: 10805 AN: 152106 Hom.: 662 Cov.: 32

Gnomad AFR AF: 0.0172

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.0997

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.0419

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0661

Gnomad OTH AF: 0.0770

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

GnomAD4 genome AF: 0.0711 AC: 10820 AN: 152224 Hom.: 665 Cov.: 32 AF XY: 0.0751 AC XY: 5587 AN XY: 74428

African (AFR) AF: 0.0172 AC: 713 AN: 41544

American (AMR) AF: 0.165 AC: 2520 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0997 AC: 346 AN: 3472

East Asian (EAS) AF: 0.211 AC: 1090 AN: 5168

South Asian (SAS) AF: 0.214 AC: 1031 AN: 4818

European-Finnish (FIN) AF: 0.0419 AC: 445 AN: 10612

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0661 AC: 4495 AN: 68000

Other (OTH) AF: 0.0772 AC: 163 AN: 2112

Alfa AF: 0.0763 Hom.: 333

Bravo AF: 0.0785

Asia WGS AF: 0.203 AC: 707 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	9.6
DANN	Benign	0.90
PhyloP100		0.82
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: rs4671993; hg19: chr2-55141989;