rs13401661

Variant names:

• chr2-54745511-C-T
• rs13401661
• NM_001039753.4:c.197+20253C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001039753.4(EML6):​c.197+20253C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 151,954 control chromosomes in the GnomAD database, including 8,122 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 0.29 (8122 hom., cov: 31)
• Consequence: EML6 NM_001039753.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627
• Publications: 3 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EML6	NM_001039753.4	c.197+20253C>T		intron_variant	Intron 2 of 41	ENST00000356458.8	NP_001034842.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EML6	ENST00000356458.8	c.197+20253C>T		intron_variant	Intron 2 of 41	5	NM_001039753.4	ENSP00000348842.6
EML6	ENST00000491655.1	n.235+20841C>T		intron_variant	Intron 2 of 3	4
EML6	ENST00000673912.1	n.197+20253C>T		intron_variant	Intron 2 of 42			ENSP00000501234.1

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43942 AN: 151836 Hom.: 8090 Cov.: 31

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.290 AC: 44027 AN: 151954 Hom.: 8122 Cov.: 31 AF XY: 0.292 AC XY: 21703 AN XY: 74298

African (AFR) AF: 0.525 AC: 21725 AN: 41408

American (AMR) AF: 0.222 AC: 3391 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.197 AC: 683 AN: 3460

East Asian (EAS) AF: 0.205 AC: 1060 AN: 5170

South Asian (SAS) AF: 0.288 AC: 1389 AN: 4816

European-Finnish (FIN) AF: 0.263 AC: 2772 AN: 10556

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.178 AC: 12128 AN: 67958

Other (OTH) AF: 0.273 AC: 577 AN: 2110

Alfa AF: 0.215 Hom.: 13256

Bravo AF: 0.293

Asia WGS AF: 0.283 AC: 983 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	0.53
DANN	Benign	0.30
PhyloP100		-0.63
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: rs13401661; hg19: chr2-54972648;