rs11949289

Variant names:

• chr5-28340066-G-A
• rs11949289

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 0.402 in 151,826 control chromosomes in the GnomAD database, including 13,823 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 0.40 (13823 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0270

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.52 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: 0.402 AC: 61012 AN: 151708 Hom.: 13821 Cov.: 31

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.0776

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.402 AC: 61032 AN: 151826 Hom.: 13823 Cov.: 31 AF XY: 0.396 AC XY: 29397 AN XY: 74184

Gnomad4 AFR AF: 0.242

Gnomad4 AMR AF: 0.354

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.0778

Gnomad4 SAS AF: 0.333

Gnomad4 FIN AF: 0.478

Gnomad4 NFE AF: 0.525

Gnomad4 OTH AF: 0.420

Alfa AF: 0.488 Hom.: 25511

Bravo AF: 0.383

Asia WGS AF: 0.196 AC: 687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11949289; hg19: chr5-28340173;