rs11120211

Variant names:

• chr1-207103034-G-A
• rs11120211

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 0.103 in 152,136 control chromosomes in the GnomAD database, including 988 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 0.10 (988 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.192 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: 0.103 AC: 15681 AN: 152018 Hom.: 988 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.0766

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.0603

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.0696

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.103 AC: 15689 AN: 152136 Hom.: 988 Cov.: 32 AF XY: 0.102 AC XY: 7622 AN XY: 74378

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.0765

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.202

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.0603

Gnomad4 NFE AF: 0.0696

Gnomad4 OTH AF: 0.119

Alfa AF: 0.0819 Hom.: 995

Bravo AF: 0.106

Asia WGS AF: 0.179 AC: 621 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.8
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11120211; hg19: chr1-207276379;