rs2450411

Variant names:

• chr11-32541262-G-A
• rs2450411

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 0.494 in 152,010 control chromosomes in the GnomAD database, including 19,507 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 0.49 (19507 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.459

ACMG classification

Verdict is Benign. Variant got -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 = 0.643 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: 0.494 AC: 75023 AN: 151892 Hom.: 19491 Cov.: 32

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.494 AC: 75080 AN: 152010 Hom.: 19507 Cov.: 32 AF XY: 0.485 AC XY: 36058 AN XY: 74294

Gnomad4 AFR AF: 0.649

Gnomad4 AMR AF: 0.402

Gnomad4 ASJ AF: 0.413

Gnomad4 EAS AF: 0.651

Gnomad4 SAS AF: 0.356

Gnomad4 FIN AF: 0.329

Gnomad4 NFE AF: 0.450

Gnomad4 OTH AF: 0.476

Alfa AF: 0.456 Hom.: 9902

Bravo AF: 0.506

Asia WGS AF: 0.519 AC: 1806 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	0.40
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2450411; hg19: chr11-32562808;