chr15-34601063-C-G

Variant names:

• chr15-34601063-C-G
• rs1820450

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 0.463 in 151,972 control chromosomes in the GnomAD database, including 17,327 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 0.46 (17327 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.395

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.542 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: 0.463 AC: 70265 AN: 151854 Hom.: 17311 Cov.: 31

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.495

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.463 AC: 70314 AN: 151972 Hom.: 17327 Cov.: 31 AF XY: 0.467 AC XY: 34710 AN XY: 74274

Gnomad4 AFR AF: 0.309

Gnomad4 AMR AF: 0.552

Gnomad4 ASJ AF: 0.553

Gnomad4 EAS AF: 0.229

Gnomad4 SAS AF: 0.501

Gnomad4 FIN AF: 0.614

Gnomad4 NFE AF: 0.523

Gnomad4 OTH AF: 0.463

Alfa AF: 0.348 Hom.: 984

Bravo AF: 0.452

Asia WGS AF: 0.385 AC: 1339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.28
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1820450; hg19: chr15-34893264;