rs1426391

Variant names:

• chr11-116072535-A-C
• rs1426391
• ENST00000765945.1:n.129+574T>G

Variant summary

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

The ENST00000765945.1(ENSG00000299737):​n.129+574T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 151,686 control chromosomes in the GnomAD database, including 12,805 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 0.39 (12805 hom., cov: 30)
• Consequence: ENSG00000299737 ENST00000765945.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.544
• Publications: 3 publications found

Genes affected

ENSG00000299737 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000765945.1. 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
	ENSG00000299737	ENST00000765945.1		n.129+574T>G		intron	N/A
	ENSG00000299737	ENST00000765946.1		n.207+479T>G		intron	N/A
	ENSG00000299737	ENST00000765947.1		n.91-5330T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.389 AC: 59025 AN: 151570 Hom.: 12797 Cov.: 30

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.389 AC: 59050 AN: 151686 Hom.: 12805 Cov.: 30 AF XY: 0.386 AC XY: 28601 AN XY: 74082

African (AFR) AF: 0.198 AC: 8183 AN: 41376

American (AMR) AF: 0.385 AC: 5863 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1585 AN: 3468

East Asian (EAS) AF: 0.393 AC: 2005 AN: 5102

South Asian (SAS) AF: 0.419 AC: 2008 AN: 4796

European-Finnish (FIN) AF: 0.455 AC: 4777 AN: 10488

Middle Eastern (MID) AF: 0.452 AC: 131 AN: 290

European-Non Finnish (NFE) AF: 0.487 AC: 33084 AN: 67910

Other (OTH) AF: 0.402 AC: 843 AN: 2096

Alfa AF: 0.436 Hom.: 28241

Bravo AF: 0.373

Asia WGS AF: 0.371 AC: 1293 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.33
DANN	Benign	0.40
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs1426391; hg19: chr11-115943253;