rs11166135

Variant names:

• chr1-98883280-A-G
• rs11166135

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 0.107 in 152,190 control chromosomes in the GnomAD database, including 1,130 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 0.11 (1130 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.259
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.232 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: 0.107 AC: 16243 AN: 152072 Hom.: 1123 Cov.: 32

Gnomad AFR AF: 0.0497

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.0758

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.107 AC: 16263 AN: 152190 Hom.: 1130 Cov.: 32 AF XY: 0.110 AC XY: 8207 AN XY: 74396

African (AFR) AF: 0.0497 AC: 2064 AN: 41546

American (AMR) AF: 0.186 AC: 2849 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0758 AC: 263 AN: 3470

East Asian (EAS) AF: 0.199 AC: 1032 AN: 5180

South Asian (SAS) AF: 0.244 AC: 1175 AN: 4822

European-Finnish (FIN) AF: 0.116 AC: 1227 AN: 10590

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7160 AN: 67978

Other (OTH) AF: 0.111 AC: 235 AN: 2116

Alfa AF: 0.107 Hom.: 836

Bravo AF: 0.110

Asia WGS AF: 0.207 AC: 716 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	2.4
DANN	Benign	0.79
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs11166135; hg19: chr1-99348836; COSMIC: COSV59977659;