11-42852452-A-G

Variant names:

• chr11-42852452-A-G
• rs4129601

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 0.0348 in 152,258 control chromosomes in the GnomAD database, including 131 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 0.035 (131 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.714
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.071 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: 0.0348 AC: 5299 AN: 152140 Hom.: 132 Cov.: 32

Gnomad AFR AF: 0.0733

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0182

Gnomad ASJ AF: 0.00980

Gnomad EAS AF: 0.0565

Gnomad SAS AF: 0.0238

Gnomad FIN AF: 0.0132

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0197

Gnomad OTH AF: 0.0287

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

GnomAD4 genome AF: 0.0348 AC: 5301 AN: 152258 Hom.: 131 Cov.: 32 AF XY: 0.0347 AC XY: 2583 AN XY: 74464

African (AFR) AF: 0.0732 AC: 3039 AN: 41536

American (AMR) AF: 0.0182 AC: 278 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.00980 AC: 34 AN: 3468

East Asian (EAS) AF: 0.0560 AC: 290 AN: 5176

South Asian (SAS) AF: 0.0238 AC: 115 AN: 4830

European-Finnish (FIN) AF: 0.0132 AC: 140 AN: 10618

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0197 AC: 1338 AN: 68012

Other (OTH) AF: 0.0284 AC: 60 AN: 2114

Alfa AF: 0.0328 Hom.: 72

Bravo AF: 0.0358

Asia WGS AF: 0.0430 AC: 149 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.27
DANN	Benign	0.72
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs4129601; hg19: chr11-42874002;