rs13401661

Positions:

• chr2-54745511-C-T

Variant summary

Our verdict is Benign. Variant got -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

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=-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/exons	MANE	UniProt
EML6	NM_001039753.4	c.197+20253C>T		intron_variant		ENST00000356458.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EML6	ENST00000356458.8	c.197+20253C>T		intron_variant		5	NM_001039753.4	P1
EML6	ENST00000673912.1	c.197+20253C>T		intron_variant, NMD_transcript_variant
EML6	ENST00000491655.1	n.235+20841C>T		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.525

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.197

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.288

Gnomad4 FIN AF: 0.263

Gnomad4 NFE AF: 0.178

Gnomad4 OTH AF: 0.273

Alfa AF: 0.195 Hom.: 6496

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

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: rs13401661; hg19: chr2-54972648;