rs1939214

Variant names:

• chr11-124735394-A-G
• rs1939214

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;