rs11633143

Positions:

• chr15-69272573-A-G

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 0.51 in 152,184 control chromosomes in the GnomAD database, including 23,409 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 (23409 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.644 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: 0.510 AC: 77604 AN: 152066 Hom.: 23410 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.649

Gnomad EAS AF: 0.588

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.646

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.510 AC: 77593 AN: 152184 Hom.: 23409 Cov.: 32 AF XY: 0.514 AC XY: 38272 AN XY: 74398

Gnomad4 AFR AF: 0.164

Gnomad4 AMR AF: 0.655

Gnomad4 ASJ AF: 0.649

Gnomad4 EAS AF: 0.588

Gnomad4 SAS AF: 0.570

Gnomad4 FIN AF: 0.648

Gnomad4 NFE AF: 0.646

Gnomad4 OTH AF: 0.545

Alfa AF: 0.567 Hom.: 3337

Bravo AF: 0.497

Asia WGS AF: 0.495 AC: 1720 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.044
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11633143; hg19: chr15-69564912;