rs11603132

Variant names:

• chr11-111231250-G-A
• rs11603132

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 0.571 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.632 AC: 26168 AN: 41414

American (AMR) AF: 0.478 AC: 7307 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.605 AC: 2101 AN: 3470

East Asian (EAS) AF: 0.322 AC: 1662 AN: 5164

South Asian (SAS) AF: 0.570 AC: 2743 AN: 4816

European-Finnish (FIN) AF: 0.574 AC: 6068 AN: 10578

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.572 AC: 38871 AN: 67978

Other (OTH) AF: 0.572 AC: 1206 AN: 2110

Alfa AF: 0.577 Hom.: 3348

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
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs11603132; hg19: chr11-111101975;