rs11216598

Variant names:

• chr11-117877737-A-G
• rs11216598

Your query was ambiguous. Multiple possible variants found:

• chr11-117877737-A-G
• chr11-117877737-A-T

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 0.145 in 152,146 control chromosomes in the GnomAD database, including 1,948 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 (1948 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.111

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.295 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: 0.145 AC: 22081 AN: 152030 Hom.: 1951 Cov.: 32

Gnomad AFR AF: 0.0716

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.145 AC: 22086 AN: 152146 Hom.: 1948 Cov.: 32 AF XY: 0.145 AC XY: 10784 AN XY: 74394

Gnomad4 AFR AF: 0.0716

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.191

Gnomad4 EAS AF: 0.300

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.166

Gnomad4 OTH AF: 0.150

Alfa AF: 0.161 Hom.: 1990

Bravo AF: 0.140

Asia WGS AF: 0.274 AC: 951 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.1
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11216598; hg19: chr11-117748452;