rs7939250

Variant names:

• chr11-69235483-G-A
• rs7939250

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 0.503 in 151,970 control chromosomes in the GnomAD database, including 20,356 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 0.50 (20356 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.234

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 (AFR) allele frequency at 95% confidence interval = 0.607 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: 0.503 AC: 76377 AN: 151852 Hom.: 20316 Cov.: 31

Gnomad AFR AF: 0.613

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.0607

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.530

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

GnomAD4 genome AF: 0.503 AC: 76469 AN: 151970 Hom.: 20356 Cov.: 31 AF XY: 0.497 AC XY: 36892 AN XY: 74276

Gnomad4 AFR AF: 0.613

Gnomad4 AMR AF: 0.389

Gnomad4 ASJ AF: 0.659

Gnomad4 EAS AF: 0.0600

Gnomad4 SAS AF: 0.323

Gnomad4 FIN AF: 0.469

Gnomad4 NFE AF: 0.505

Gnomad4 OTH AF: 0.527

Alfa AF: 0.460 Hom.: 3538

Bravo AF: 0.504

Asia WGS AF: 0.289 AC: 1006 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	0.50
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: rs7939250; hg19: chr11-69002950;