rs1820450

Positions:

• chr15-34601063-C-G
• chr15-34601063-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;