chr15-34697425-G-T

Variant names:

• chr15-34697425-G-T
• rs11073058

Variant summary

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

The variant allele was found at a frequency of 0.408 in 152,020 control chromosomes in the GnomAD database, including 12,828 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 0.41 (12828 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.571 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

Frequencies

GnomAD3 genomes AF: 0.409 AC: 62063 AN: 151902 Hom.: 12824 Cov.: 33

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.408 AC: 62098 AN: 152020 Hom.: 12828 Cov.: 33 AF XY: 0.407 AC XY: 30258 AN XY: 74318

Gnomad4 AFR AF: 0.378

Gnomad4 AMR AF: 0.372

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.440

Gnomad4 SAS AF: 0.589

Gnomad4 FIN AF: 0.348

Gnomad4 NFE AF: 0.430

Gnomad4 OTH AF: 0.406

Alfa AF: 0.411 Hom.: 11483

Bravo AF: 0.405

Asia WGS AF: 0.515 AC: 1791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11073058; hg19: chr15-34989626;