rs1266270

Variant names:

• chr14-45626687-A-G
• rs1266270
• ENST00000837756.1:n.131+186A>G

Variant summary

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

The ENST00000837756.1(ENSG00000309007):​n.131+186A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 152,038 control chromosomes in the GnomAD database, including 10,376 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 0.34 (10376 hom., cov: 32)
• Consequence: ENSG00000309007 ENST00000837756.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.397
• Publications: 1 publications found

Genes affected

ENSG00000309007 (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 (EAS) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309007	ENST00000837756.1	n.131+186A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51950 AN: 151920 Hom.: 10375 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.628

Gnomad SAS AF: 0.479

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.342 AC: 51946 AN: 152038 Hom.: 10376 Cov.: 32 AF XY: 0.343 AC XY: 25489 AN XY: 74284

African (AFR) AF: 0.138 AC: 5717 AN: 41506

American (AMR) AF: 0.302 AC: 4606 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1460 AN: 3466

East Asian (EAS) AF: 0.628 AC: 3244 AN: 5162

South Asian (SAS) AF: 0.480 AC: 2308 AN: 4810

European-Finnish (FIN) AF: 0.427 AC: 4499 AN: 10548

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.426 AC: 28959 AN: 67954

Other (OTH) AF: 0.325 AC: 687 AN: 2112

Alfa AF: 0.385 Hom.: 4237

Bravo AF: 0.321

Asia WGS AF: 0.530 AC: 1843 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	10
DANN	Benign	0.64
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs1266270; hg19: chr14-46095890;