rs7116722

Variant names:

• chr11-58739435-C-A
• rs7116722

Your query was ambiguous. Multiple possible variants found:

• chr11-58739435-C-A
• chr11-58739435-C-T

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 0.0301 in 152,206 control chromosomes in the GnomAD database, including 89 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 0.030 (89 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.193
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0586 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0301 AC: 4574 AN: 152088 Hom.: 89 Cov.: 31

Gnomad AFR AF: 0.0605

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0139

Gnomad ASJ AF: 0.0297

Gnomad EAS AF: 0.0359

Gnomad SAS AF: 0.0460

Gnomad FIN AF: 0.00340

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0183

Gnomad OTH AF: 0.0211

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

GnomAD4 genome AF: 0.0301 AC: 4582 AN: 152206 Hom.: 89 Cov.: 31 AF XY: 0.0294 AC XY: 2189 AN XY: 74418

African (AFR) AF: 0.0606 AC: 2515 AN: 41524

American (AMR) AF: 0.0138 AC: 211 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0297 AC: 103 AN: 3470

East Asian (EAS) AF: 0.0356 AC: 184 AN: 5174

South Asian (SAS) AF: 0.0456 AC: 220 AN: 4824

European-Finnish (FIN) AF: 0.00340 AC: 36 AN: 10602

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0184 AC: 1248 AN: 68008

Other (OTH) AF: 0.0218 AC: 46 AN: 2110

Alfa AF: 0.0240 Hom.: 74

Bravo AF: 0.0330

Asia WGS AF: 0.0450 AC: 157 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	11
DANN	Benign	0.91
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs7116722; hg19: chr11-58506908;