chr1-207103034-G-A

Variant names:

• chr1-207103034-G-A
• rs11120211

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 0.103 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
• Publications: 21 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.103 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

African (AFR) AF: 0.161 AC: 6687 AN: 41480

American (AMR) AF: 0.0765 AC: 1170 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 431 AN: 3470

East Asian (EAS) AF: 0.202 AC: 1045 AN: 5176

South Asian (SAS) AF: 0.129 AC: 621 AN: 4820

European-Finnish (FIN) AF: 0.0603 AC: 638 AN: 10584

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.0696 AC: 4731 AN: 68004

Other (OTH) AF: 0.119 AC: 252 AN: 2110

Alfa AF: 0.0867 Hom.: 1899

Bravo AF: 0.106

Asia WGS AF: 0.179 AC: 621 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.8
DANN	Benign	0.58
PhyloP100		-0.090

Splicing

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

Other links and lift over

dbSNP: rs11120211; hg19: chr1-207276379;