rs1189402

Positions:

• 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, non coding transcript 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: ENST00000662193.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.175

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000662193.1	n.805+15288A>G		intron_variant, non_coding_transcript_variant

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;