rs11165059

Variant names:

• chr1-91602396-G-A
• rs11165059

Your query was ambiguous. Multiple possible variants found:

• chr1-91602396-G-A
• chr1-91602396-G-T

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 0.171 in 152,112 control chromosomes in the GnomAD database, including 2,744 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 0.17 (2744 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.396
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.221 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: 0.171 AC: 25952 AN: 151994 Hom.: 2743 Cov.: 32

Gnomad AFR AF: 0.0844

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0673

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.171 AC: 25965 AN: 152112 Hom.: 2744 Cov.: 32 AF XY: 0.172 AC XY: 12768 AN XY: 74358

African (AFR) AF: 0.0844 AC: 3504 AN: 41518

American (AMR) AF: 0.141 AC: 2157 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 719 AN: 3464

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5178

South Asian (SAS) AF: 0.0678 AC: 327 AN: 4822

European-Finnish (FIN) AF: 0.323 AC: 3421 AN: 10576

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.224 AC: 15234 AN: 67954

Other (OTH) AF: 0.176 AC: 371 AN: 2108

Alfa AF: 0.0971 Hom.: 171

Bravo AF: 0.154

Asia WGS AF: 0.0400 AC: 139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	4.1
DANN	Benign	0.88
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs11165059; hg19: chr1-92067953;