rs1954783

Variant names:

• chr11-93613320-T-C
• rs1954783

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 0.439 in 152,022 control chromosomes in the GnomAD database, including 15,194 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 (15194 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.273

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.562 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: 0.439 AC: 66700 AN: 151904 Hom.: 15182 Cov.: 32

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.439 AC: 66729 AN: 152022 Hom.: 15194 Cov.: 32 AF XY: 0.440 AC XY: 32730 AN XY: 74324

Gnomad4 AFR AF: 0.332

Gnomad4 AMR AF: 0.572

Gnomad4 ASJ AF: 0.520

Gnomad4 EAS AF: 0.475

Gnomad4 SAS AF: 0.507

Gnomad4 FIN AF: 0.419

Gnomad4 NFE AF: 0.464

Gnomad4 OTH AF: 0.425

Alfa AF: 0.466 Hom.: 21669

Bravo AF: 0.446

Asia WGS AF: 0.453 AC: 1577 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.8
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1954783; hg19: chr11-93346486;