rs11238214

Variant names:

• chr7-50568321-A-G
• rs11238214

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.340 AC: 14101 AN: 41496

American (AMR) AF: 0.320 AC: 4887 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 992 AN: 3468

East Asian (EAS) AF: 0.587 AC: 3035 AN: 5168

South Asian (SAS) AF: 0.471 AC: 2271 AN: 4824

European-Finnish (FIN) AF: 0.539 AC: 5707 AN: 10582

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.353 AC: 24005 AN: 67974

Other (OTH) AF: 0.326 AC: 689 AN: 2112

Alfa AF: 0.369 Hom.: 1335

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
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs11238214; hg19: chr7-50636018;