rs11990854

Variant names:

• chr8-49079489-T-C
• rs11990854

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 0.503 in 152,028 control chromosomes in the GnomAD database, including 20,293 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 0.50 (20293 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.75

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.802 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: 0.503 AC: 76455 AN: 151910 Hom.: 20264 Cov.: 32

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.823

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.634

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.503 AC: 76516 AN: 152028 Hom.: 20293 Cov.: 32 AF XY: 0.511 AC XY: 37965 AN XY: 74280

Gnomad4 AFR AF: 0.342

Gnomad4 AMR AF: 0.606

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.823

Gnomad4 SAS AF: 0.451

Gnomad4 FIN AF: 0.634

Gnomad4 NFE AF: 0.540

Gnomad4 OTH AF: 0.516

Alfa AF: 0.510 Hom.: 2504

Bravo AF: 0.501

Asia WGS AF: 0.596 AC: 2071 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.065
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11990854; hg19: chr8-49992048;