rs2450254

Positions:

• chr11-69635016-A-T

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 0.445 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

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 (AFR) allele frequency at 95% confidence interval = 0.534 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: 0.445 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

Gnomad4 AFR AF: 0.540

Gnomad4 AMR AF: 0.525

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.365

Gnomad4 FIN AF: 0.365

Gnomad4 NFE AF: 0.409

Gnomad4 OTH AF: 0.441

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2450254; hg19: chr11-69449784;