rs2011603

Variant names:

• chr4-18023861-G-A
• rs2011603

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 0.704 in 152,070 control chromosomes in the GnomAD database, including 37,982 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 0.70 (37982 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.343
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.831 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: 0.704 AC: 107005 AN: 151952 Hom.: 37936 Cov.: 32

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.782

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.759

Gnomad EAS AF: 0.535

Gnomad SAS AF: 0.852

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.739

Gnomad OTH AF: 0.703

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

GnomAD4 genome AF: 0.704 AC: 107109 AN: 152070 Hom.: 37982 Cov.: 32 AF XY: 0.701 AC XY: 52126 AN XY: 74344

African (AFR) AF: 0.666 AC: 27636 AN: 41468

American (AMR) AF: 0.663 AC: 10130 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.759 AC: 2629 AN: 3466

East Asian (EAS) AF: 0.536 AC: 2763 AN: 5154

South Asian (SAS) AF: 0.852 AC: 4112 AN: 4824

European-Finnish (FIN) AF: 0.681 AC: 7199 AN: 10566

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.739 AC: 50215 AN: 67986

Other (OTH) AF: 0.705 AC: 1491 AN: 2114

Alfa AF: 0.712 Hom.: 15261

Bravo AF: 0.695

Asia WGS AF: 0.703 AC: 2448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.63
DANN	Benign	0.38
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs2011603; hg19: chr4-18025484;