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. The variant received -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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.902 AC: 37478 AN: 41528

American (AMR) AF: 0.742 AC: 11339 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.647 AC: 2247 AN: 3472

East Asian (EAS) AF: 0.872 AC: 4512 AN: 5176

South Asian (SAS) AF: 0.668 AC: 3219 AN: 4816

European-Finnish (FIN) AF: 0.556 AC: 5861 AN: 10550

Middle Eastern (MID) AF: 0.712 AC: 208 AN: 292

European-Non Finnish (NFE) AF: 0.564 AC: 38330 AN: 67988

Other (OTH) AF: 0.706 AC: 1492 AN: 2114

Alfa AF: 0.608 Hom.: 94314

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
PhyloP100		0.040

Splicing

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

Other links and lift over

dbSNP: rs1015363; hg19: chr20-32738335;