rs6726292

Variant names:

• chr2-54929493-G-A
• rs6726292
• NM_001039753.4:c.4004+742G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-54929493-G-A
• chr2-54929493-G-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.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
• Publications: 8 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=-0.92).
• 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 rank	MANE	Protein	UniProt
EML6	NM_001039753.4	c.4004+742G>A		intron_variant	Intron 28 of 41	ENST00000356458.8	NP_001034842.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EML6	ENST00000356458.8	c.4004+742G>A		intron_variant	Intron 28 of 41	5	NM_001039753.4	ENSP00000348842.6
EML6	ENST00000673912.1	n.4004+742G>A		intron_variant	Intron 28 of 42			ENSP00000501234.1

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

African (AFR) AF: 0.391 AC: 16186 AN: 41436

American (AMR) AF: 0.342 AC: 5236 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 910 AN: 3468

East Asian (EAS) AF: 0.256 AC: 1329 AN: 5184

South Asian (SAS) AF: 0.514 AC: 2480 AN: 4824

European-Finnish (FIN) AF: 0.259 AC: 2729 AN: 10552

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.277 AC: 18844 AN: 67972

Other (OTH) AF: 0.311 AC: 654 AN: 2106

Alfa AF: 0.291 Hom.: 16173

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
PhyloP100		-0.18
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: rs6726292; hg19: chr2-55156630;