chr11-44258540-C-T

Variant names:

• chr11-44258540-C-T
• rs729287

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 0.247 in 152,210 control chromosomes in the GnomAD database, including 5,819 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 0.25 (5819 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.43 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: 0.247 AC: 37613 AN: 152092 Hom.: 5799 Cov.: 33

Gnomad AFR AF: 0.0941

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.247 AC: 37648 AN: 152210 Hom.: 5819 Cov.: 33 AF XY: 0.255 AC XY: 18999 AN XY: 74428

Gnomad4 AFR AF: 0.0940

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.445

Gnomad4 SAS AF: 0.370

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.272

Alfa AF: 0.242 Hom.: 2354

Bravo AF: 0.249

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.1
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs729287; hg19: chr11-44280090;