rs11722450

Variant names:

• chr4-118387448-T-C
• rs11722450

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 0.153 in 151,890 control chromosomes in the GnomAD database, including 2,111 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 0.15 (2111 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.767

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.201 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: 0.153 AC: 23196 AN: 151776 Hom.: 2114 Cov.: 31

Gnomad AFR AF: 0.0370

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.0772

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.153 AC: 23196 AN: 151890 Hom.: 2111 Cov.: 31 AF XY: 0.156 AC XY: 11585 AN XY: 74224

Gnomad4 AFR AF: 0.0370

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.0764

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.270

Gnomad4 NFE AF: 0.204

Gnomad4 OTH AF: 0.152

Alfa AF: 0.180 Hom.: 621

Bravo AF: 0.137

Asia WGS AF: 0.135 AC: 468 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.5
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11722450; hg19: chr4-119308603;