rs11603132

chr11-111231250-G-A

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 0.571 in 152,024 control chromosomes in the GnomAD database, including 25,144 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 0.57 (25144 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.658

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.571 AC: 86780 AN: 151906 Hom.: 25144 Cov.: 32

Gnomad AFR AF: 0.632

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.571 AC: 86801 AN: 152024 Hom.: 25144 Cov.: 32 AF XY: 0.566 AC XY: 42088 AN XY: 74310

Gnomad4 AFR AF: 0.632

Gnomad4 AMR AF: 0.478

Gnomad4 ASJ AF: 0.605

Gnomad4 EAS AF: 0.322

Gnomad4 SAS AF: 0.570

Gnomad4 FIN AF: 0.574

Gnomad4 NFE AF: 0.572

Gnomad4 OTH AF: 0.572

Alfa AF: 0.575 Hom.: 3200

Bravo AF: 0.564

Asia WGS AF: 0.467 AC: 1625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.52
Dann	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11603132; hg19: chr11-111101975;