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. The variant received -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
• Publications: 10 publications found

Genes affected

ENSG00000287596 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000662193.1. 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
	ENSG00000287596	ENST00000662193.1		n.805+15288A>G		intron	N/A
	ENSG00000287596	ENST00000851014.1		n.344+15288A>G		intron	N/A

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

African (AFR) AF: 0.235 AC: 9639 AN: 41032

American (AMR) AF: 0.292 AC: 4416 AN: 15110

Ashkenazi Jewish (ASJ) AF: 0.299 AC: 1032 AN: 3456

East Asian (EAS) AF: 0.148 AC: 756 AN: 5122

South Asian (SAS) AF: 0.219 AC: 1041 AN: 4758

European-Finnish (FIN) AF: 0.406 AC: 4180 AN: 10286

Middle Eastern (MID) AF: 0.441 AC: 128 AN: 290

European-Non Finnish (NFE) AF: 0.377 AC: 25570 AN: 67856

Other (OTH) AF: 0.327 AC: 685 AN: 2092

Alfa AF: 0.353 Hom.: 43067

Bravo AF: 0.306

Asia WGS AF: 0.152 AC: 535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	4.9
DANN	Benign	0.87
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs1189402; hg19: chr15-53728154;