rs1189402

Variant names:

• chr15-53435957-A-G
• rs1189402
• ENST00000662193.1:n.805+15288A>G

Your query was ambiguous. Multiple possible variants found:

• chr15-53435957-A-G
• chr15-53435957-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000662193.1(ENSG00000287596):​n.805+15288A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 150,904 control chromosomes in the GnomAD database, including 7,991 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 0.32 (7991 hom., cov: 31)
• Consequence: ENSG00000287596 ENST00000662193.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.175

Genes affected

ENSG00000287596 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.373 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
ENSG00000287596	ENST00000662193.1	n.805+15288A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.318 AC: 47968 AN: 150794 Hom.: 7996 Cov.: 31

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.318 AC: 47956 AN: 150904 Hom.: 7991 Cov.: 31 AF XY: 0.317 AC XY: 23339 AN XY: 73618

Gnomad4 AFR AF: 0.235

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.299

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.377

Gnomad4 OTH AF: 0.327

Alfa AF: 0.359 Hom.: 20671

Bravo AF: 0.306

Asia WGS AF: 0.152 AC: 535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	4.9
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1189402; hg19: chr15-53728154;