rs7122785

Positions:

• chr11-119351996-G-A

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 0.681 in 152,034 control chromosomes in the GnomAD database, including 35,918 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 0.68 (35918 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.826 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.681 AC: 103522 AN: 151916 Hom.: 35889 Cov.: 32

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.819

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.847

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.788

Gnomad MID AF: 0.799

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.681 AC: 103592 AN: 152034 Hom.: 35918 Cov.: 32 AF XY: 0.687 AC XY: 51072 AN XY: 74306

Gnomad4 AFR AF: 0.565

Gnomad4 AMR AF: 0.622

Gnomad4 ASJ AF: 0.702

Gnomad4 EAS AF: 0.847

Gnomad4 SAS AF: 0.780

Gnomad4 FIN AF: 0.788

Gnomad4 NFE AF: 0.726

Gnomad4 OTH AF: 0.687

Alfa AF: 0.721 Hom.: 61651

Bravo AF: 0.668

Asia WGS AF: 0.798 AC: 2773 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.035
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7122785; hg19: chr11-119222706;