rs1108001

Variant names:

• chr11-20277252-G-A
• rs1108001

Your query was ambiguous. Multiple possible variants found:

• chr11-20277252-G-A
• chr11-20277252-G-C
• chr11-20277252-G-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.522 in 151,912 control chromosomes in the GnomAD database, including 21,246 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 0.52 (21246 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.21
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.32).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.839 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: 0.521 AC: 79147 AN: 151794 Hom.: 21214 Cov.: 32

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.861

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.522 AC: 79233 AN: 151912 Hom.: 21246 Cov.: 32 AF XY: 0.531 AC XY: 39413 AN XY: 74254

African (AFR) AF: 0.574 AC: 23773 AN: 41404

American (AMR) AF: 0.512 AC: 7810 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.399 AC: 1387 AN: 3472

East Asian (EAS) AF: 0.861 AC: 4430 AN: 5148

South Asian (SAS) AF: 0.631 AC: 3040 AN: 4814

European-Finnish (FIN) AF: 0.542 AC: 5729 AN: 10562

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.463 AC: 31471 AN: 67938

Other (OTH) AF: 0.506 AC: 1065 AN: 2104

Alfa AF: 0.472 Hom.: 28776

Bravo AF: 0.517

Asia WGS AF: 0.730 AC: 2540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
CADD	Benign	20
DANN	Benign	0.86
PhyloP100		4.2

Splicing

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

Other links and lift over

dbSNP: rs1108001; hg19: chr11-20298798;