rs11157248

chr14-21821498-T-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 0.175 in 152,096 control chromosomes in the GnomAD database, including 2,706 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 0.17 (2706 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.284

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.227 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: 0.175 AC: 26607 AN: 151978 Hom.: 2708 Cov.: 31

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.0595

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.175 AC: 26604 AN: 152096 Hom.: 2706 Cov.: 31 AF XY: 0.173 AC XY: 12864 AN XY: 74348

Gnomad4 AFR AF: 0.100

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.180

Gnomad4 EAS AF: 0.0596

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.240

Gnomad4 NFE AF: 0.230

Gnomad4 OTH AF: 0.165

Alfa AF: 0.210 Hom.: 697

Bravo AF: 0.165

Asia WGS AF: 0.100 AC: 349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	9.6
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11157248; hg19: chr14-22289663;