rs2450411

Variant names:

• chr11-32541262-G-A
• rs2450411

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 0.494 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.649 AC: 26924 AN: 41456

American (AMR) AF: 0.402 AC: 6130 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1433 AN: 3468

East Asian (EAS) AF: 0.651 AC: 3359 AN: 5156

South Asian (SAS) AF: 0.356 AC: 1719 AN: 4822

European-Finnish (FIN) AF: 0.329 AC: 3477 AN: 10570

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.450 AC: 30580 AN: 67966

Other (OTH) AF: 0.476 AC: 1005 AN: 2112

Alfa AF: 0.462 Hom.: 13901

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
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs2450411; hg19: chr11-32562808;