rs11238214

chr7-50568321-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 0.369 in 152,118 control chromosomes in the GnomAD database, including 10,835 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 0.37 (10835 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.197

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.57 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: 0.368 AC: 56001 AN: 152000 Hom.: 10811 Cov.: 33

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.369 AC: 56063 AN: 152118 Hom.: 10835 Cov.: 33 AF XY: 0.381 AC XY: 28340 AN XY: 74366

Gnomad4 AFR AF: 0.340

Gnomad4 AMR AF: 0.320

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.587

Gnomad4 SAS AF: 0.471

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.353

Gnomad4 OTH AF: 0.326

Alfa AF: 0.352 Hom.: 868

Bravo AF: 0.353

Asia WGS AF: 0.469 AC: 1632 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.9
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11238214; hg19: chr7-50636018;