rs1476203

chr11-123944046-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 0.768 in 152,186 control chromosomes in the GnomAD database, including 44,980 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 0.77 (44980 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.172

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.778 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: 0.768 AC: 116769 AN: 152068 Hom.: 44953 Cov.: 33

Gnomad AFR AF: 0.772

Gnomad AMI AF: 0.814

Gnomad AMR AF: 0.724

Gnomad ASJ AF: 0.819

Gnomad EAS AF: 0.641

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.784

Gnomad OTH AF: 0.766

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

GnomAD4 genome AF: 0.768 AC: 116844 AN: 152186 Hom.: 44980 Cov.: 33 AF XY: 0.764 AC XY: 56857 AN XY: 74400

Gnomad4 AFR AF: 0.772

Gnomad4 AMR AF: 0.724

Gnomad4 ASJ AF: 0.819

Gnomad4 EAS AF: 0.641

Gnomad4 SAS AF: 0.670

Gnomad4 FIN AF: 0.797

Gnomad4 NFE AF: 0.784

Gnomad4 OTH AF: 0.760

Alfa AF: 0.790 Hom.: 73087

Bravo AF: 0.765

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	5.9
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1476203; hg19: chr11-123814753;