chr11-1217598-T-G

Variant names:

• chr11-1217598-T-G
• rs7120886

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 0.31 in 151,316 control chromosomes in the GnomAD database, including 8,224 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 0.31 (8224 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.478 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46793 AN: 151196 Hom.: 8196 Cov.: 31

Gnomad AFR AF: 0.483

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.310 AC: 46873 AN: 151316 Hom.: 8224 Cov.: 31 AF XY: 0.309 AC XY: 22821 AN XY: 73902

African (AFR) AF: 0.484 AC: 19958 AN: 41258

American (AMR) AF: 0.215 AC: 3272 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 618 AN: 3470

East Asian (EAS) AF: 0.102 AC: 525 AN: 5122

South Asian (SAS) AF: 0.244 AC: 1163 AN: 4766

European-Finnish (FIN) AF: 0.292 AC: 3052 AN: 10454

Middle Eastern (MID) AF: 0.247 AC: 72 AN: 292

European-Non Finnish (NFE) AF: 0.256 AC: 17339 AN: 67758

Other (OTH) AF: 0.307 AC: 644 AN: 2096

Alfa AF: 0.275 Hom.: 17286

Bravo AF: 0.308

Asia WGS AF: 0.224 AC: 781 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.67
DANN	Benign	0.55
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs7120886; hg19: chr11-1238828;