rs11949289

Positions:

• chr5-28340066-G-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;