rs1939214

chr11-124735394-A-G

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 0.181 in 152,132 control chromosomes in the GnomAD database, including 2,621 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 0.18 (2621 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.233 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: 0.180 AC: 27407 AN: 152012 Hom.: 2608 Cov.: 32

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.0935

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.181 AC: 27471 AN: 152132 Hom.: 2621 Cov.: 32 AF XY: 0.177 AC XY: 13147 AN XY: 74388

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.119

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.0934

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.182

Alfa AF: 0.166 Hom.: 3787

Bravo AF: 0.181

Asia WGS AF: 0.198 AC: 692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	8.0
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1939214; hg19: chr11-124605290;