rs1466408

Variant names:

• chr2-156348594-T-A
• rs1466408
• ENST00000840148.1:n.104+6678T>A

Variant summary

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

The ENST00000840148.1(ENSG00000309294):​n.104+6678T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 152,232 control chromosomes in the GnomAD database, including 2,396 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 0.14 (2396 hom., cov: 33)
• Consequence: ENSG00000309294 ENST00000840148.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.41
• Publications: 3 publications found

Genes affected

ENSG00000309294 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000840148.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309294	ENST00000840148.1		n.104+6678T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21177 AN: 152112 Hom.: 2392 Cov.: 33

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.0957

Gnomad ASJ AF: 0.0352

Gnomad EAS AF: 0.00327

Gnomad SAS AF: 0.0701

Gnomad FIN AF: 0.0626

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0768

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.139 AC: 21213 AN: 152232 Hom.: 2396 Cov.: 33 AF XY: 0.135 AC XY: 10064 AN XY: 74438

African (AFR) AF: 0.315 AC: 13054 AN: 41484

American (AMR) AF: 0.0958 AC: 1466 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0352 AC: 122 AN: 3470

East Asian (EAS) AF: 0.00327 AC: 17 AN: 5192

South Asian (SAS) AF: 0.0695 AC: 336 AN: 4832

European-Finnish (FIN) AF: 0.0626 AC: 664 AN: 10614

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0768 AC: 5221 AN: 68024

Other (OTH) AF: 0.109 AC: 230 AN: 2112

Alfa AF: 0.117 Hom.: 211

Bravo AF: 0.151

Asia WGS AF: 0.0490 AC: 170 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	13
DANN	Benign	0.72
PhyloP100		1.4

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1466408;

hg19: chr2-157205106;