rs11071529

Variant names:

• chr15-60417705-G-A
• rs11071529

Your query was ambiguous. Multiple possible variants found:

• chr15-60417705-G-A
• chr15-60417705-G-C

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 0.505 in 151,974 control chromosomes in the GnomAD database, including 21,857 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 0.51 (21857 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.815 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: 0.505 AC: 76736 AN: 151856 Hom.: 21838 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.707

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.306

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.505 AC: 76773 AN: 151974 Hom.: 21857 Cov.: 32 AF XY: 0.519 AC XY: 38515 AN XY: 74262

African (AFR) AF: 0.238 AC: 9851 AN: 41436

American (AMR) AF: 0.587 AC: 8977 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1726 AN: 3470

East Asian (EAS) AF: 0.836 AC: 4315 AN: 5164

South Asian (SAS) AF: 0.779 AC: 3755 AN: 4818

European-Finnish (FIN) AF: 0.714 AC: 7522 AN: 10540

Middle Eastern (MID) AF: 0.315 AC: 92 AN: 292

European-Non Finnish (NFE) AF: 0.572 AC: 38858 AN: 67952

Other (OTH) AF: 0.490 AC: 1032 AN: 2108

Alfa AF: 0.543 Hom.: 38408

Bravo AF: 0.480

Asia WGS AF: 0.778 AC: 2702 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.44
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs11071529; hg19: chr15-60709904;