rs4529869

Variant names:

• chr11-2123215-G-A
• rs4529869

Your query was ambiguous. Multiple possible variants found:

• chr11-2123215-G-A
• chr11-2123215-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 0.409 in 149,130 control chromosomes in the GnomAD database, including 13,963 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 0.41 (13963 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.662
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.547 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: 0.409 AC: 60978 AN: 149016 Hom.: 13946 Cov.: 27

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.322

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.409 AC: 61021 AN: 149130 Hom.: 13963 Cov.: 27 AF XY: 0.409 AC XY: 29717 AN XY: 72678

African (AFR) AF: 0.212 AC: 8663 AN: 40792

American (AMR) AF: 0.557 AC: 8326 AN: 14942

Ashkenazi Jewish (ASJ) AF: 0.428 AC: 1473 AN: 3440

East Asian (EAS) AF: 0.306 AC: 1515 AN: 4950

South Asian (SAS) AF: 0.331 AC: 1548 AN: 4678

European-Finnish (FIN) AF: 0.483 AC: 4842 AN: 10028

Middle Eastern (MID) AF: 0.308 AC: 90 AN: 292

European-Non Finnish (NFE) AF: 0.495 AC: 33148 AN: 67032

Other (OTH) AF: 0.412 AC: 858 AN: 2080

Alfa AF: 0.219 Hom.: 370

Bravo AF: 0.409

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.32
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs4529869; hg19: chr11-2144445;