rs2450254

Variant names:

• chr11-69635016-A-T
• rs2450254

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 0.445 in 151,942 control chromosomes in the GnomAD database, including 15,670 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 0.44 (15670 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.56
• Publications: 8 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 (AFR) allele frequency at 95% confidence interval = 0.534 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: 0.445 AC: 67540 AN: 151828 Hom.: 15646 Cov.: 32

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.494

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.445 AC: 67609 AN: 151942 Hom.: 15670 Cov.: 32 AF XY: 0.441 AC XY: 32721 AN XY: 74248

African (AFR) AF: 0.540 AC: 22358 AN: 41428

American (AMR) AF: 0.525 AC: 8023 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1425 AN: 3468

East Asian (EAS) AF: 0.171 AC: 887 AN: 5176

South Asian (SAS) AF: 0.365 AC: 1753 AN: 4802

European-Finnish (FIN) AF: 0.365 AC: 3838 AN: 10518

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.409 AC: 27815 AN: 67962

Other (OTH) AF: 0.441 AC: 930 AN: 2110

Alfa AF: 0.425 Hom.: 1779

Bravo AF: 0.462

Asia WGS AF: 0.321 AC: 1118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.0050
DANN	Benign	0.44
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs2450254; hg19: chr11-69449784;