rs7120886

chr11-1217598-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 0.31 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.309 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

Gnomad4 AFR AF: 0.484

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.307

Alfa AF: 0.262 Hom.: 9557

Bravo AF: 0.308

Asia WGS AF: 0.224 AC: 781 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.67
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7120886; hg19: chr11-1238828;