rs1599459

Variant names:

• chr11-39029342-C-T
• rs1599459
• ENST00000649415.2:n.437-2538G>A

Variant summary

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

The ENST00000649415.2(ENSG00000285751):​n.437-2538G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 151,968 control chromosomes in the GnomAD database, including 9,907 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 0.33 (9907 hom., cov: 32)
• Consequence: ENSG00000285751 ENST00000649415.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928
• Publications: 0 publications found

Genes affected

ENSG00000285751 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649415.2. 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
	ENSG00000285751	ENST00000649415.2		n.437-2538G>A		intron	N/A
	ENSG00000285751	ENST00000722718.1		n.438+91247G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49489 AN: 151850 Hom.: 9898 Cov.: 32

Gnomad AFR AF: 0.0825

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.326 AC: 49507 AN: 151968 Hom.: 9907 Cov.: 32 AF XY: 0.328 AC XY: 24361 AN XY: 74278

African (AFR) AF: 0.0823 AC: 3415 AN: 41482

American (AMR) AF: 0.435 AC: 6643 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1362 AN: 3468

East Asian (EAS) AF: 0.378 AC: 1943 AN: 5140

South Asian (SAS) AF: 0.379 AC: 1822 AN: 4808

European-Finnish (FIN) AF: 0.381 AC: 4020 AN: 10560

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.428 AC: 29058 AN: 67938

Other (OTH) AF: 0.353 AC: 743 AN: 2106

Alfa AF: 0.391 Hom.: 38288

Bravo AF: 0.319

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.059
DANN	Benign	0.67
PhyloP100		-0.93

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: rs1599459;

hg19: chr11-39050892;