chr15-34697473-T-A

Position:

• chr15-34697473-T-A

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 152,050 control chromosomes in the GnomAD database, including 12,826 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 (12826 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.860

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.408 AC: 62058 AN: 151932 Hom.: 12822 Cov.: 33

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.408 AC: 62093 AN: 152050 Hom.: 12826 Cov.: 33 AF XY: 0.407 AC XY: 30243 AN XY: 74336

Gnomad4 AFR AF: 0.378

Gnomad4 AMR AF: 0.373

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.440

Gnomad4 SAS AF: 0.589

Gnomad4 FIN AF: 0.347

Gnomad4 NFE AF: 0.430

Gnomad4 OTH AF: 0.405

Alfa AF: 0.405 Hom.: 1569

Bravo AF: 0.405

Asia WGS AF: 0.515 AC: 1792 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.65
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11073059; hg19: chr15-34989674;