rs4939287

Positions:

• chr11-59382169-T-A
• chr11-59382169-T-C

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 0.23 in 152,068 control chromosomes in the GnomAD database, including 4,935 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 0.23 (4935 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.109

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 (AMR) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34943 AN: 151950 Hom.: 4939 Cov.: 31

Gnomad AFR AF: 0.0604

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.230 AC: 34932 AN: 152068 Hom.: 4935 Cov.: 31 AF XY: 0.231 AC XY: 17138 AN XY: 74314

Gnomad4 AFR AF: 0.0602

Gnomad4 AMR AF: 0.310

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.155

Gnomad4 SAS AF: 0.248

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.306

Gnomad4 OTH AF: 0.227

Alfa AF: 0.142 Hom.: 280

Bravo AF: 0.224

Asia WGS AF: 0.176 AC: 612 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	2.5
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4939287; hg19: chr11-59149642;