rs1015363

Variant names:

• chr20-34150529-G-A
• rs1015363

Your query was ambiguous. Multiple possible variants found:

• chr20-34150529-G-A
• chr20-34150529-G-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 0.693 in 152,130 control chromosomes in the GnomAD database, including 38,257 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 0.69 (38257 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0400

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 (AFR) allele frequency at 95% confidence interval = 0.895 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: 0.692 AC: 105261 AN: 152012 Hom.: 38199 Cov.: 32

Gnomad AFR AF: 0.902

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.647

Gnomad EAS AF: 0.870

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.717

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.711

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

GnomAD4 genome AF: 0.693 AC: 105371 AN: 152130 Hom.: 38257 Cov.: 32 AF XY: 0.694 AC XY: 51620 AN XY: 74368

Gnomad4 AFR AF: 0.902

Gnomad4 AMR AF: 0.742

Gnomad4 ASJ AF: 0.647

Gnomad4 EAS AF: 0.872

Gnomad4 SAS AF: 0.668

Gnomad4 FIN AF: 0.556

Gnomad4 NFE AF: 0.564

Gnomad4 OTH AF: 0.706

Alfa AF: 0.584 Hom.: 36323

Bravo AF: 0.718

Asia WGS AF: 0.761 AC: 2647 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	4.5
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1015363; hg19: chr20-32738335;