rs4245843

Variant names:

• chr2-136282214-A-G
• rs4245843

Your query was ambiguous. Multiple possible variants found:

• chr2-136282214-A-G
• chr2-136282214-A-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 0.807 in 151,624 control chromosomes in the GnomAD database, including 51,442 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 0.81 (51442 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.262
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.932 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: 0.807 AC: 122328 AN: 151508 Hom.: 51440 Cov.: 29

Gnomad AFR AF: 0.557

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.884

Gnomad EAS AF: 0.768

Gnomad SAS AF: 0.830

Gnomad FIN AF: 0.948

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.938

Gnomad OTH AF: 0.811

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

GnomAD4 genome AF: 0.807 AC: 122359 AN: 151624 Hom.: 51442 Cov.: 29 AF XY: 0.806 AC XY: 59698 AN XY: 74084

African (AFR) AF: 0.556 AC: 22956 AN: 41278

American (AMR) AF: 0.785 AC: 11977 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.884 AC: 3066 AN: 3468

East Asian (EAS) AF: 0.767 AC: 3940 AN: 5134

South Asian (SAS) AF: 0.830 AC: 3993 AN: 4808

European-Finnish (FIN) AF: 0.948 AC: 9956 AN: 10504

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.938 AC: 63626 AN: 67858

Other (OTH) AF: 0.811 AC: 1712 AN: 2110

Alfa AF: 0.876 Hom.: 41297

Bravo AF: 0.782

Asia WGS AF: 0.734 AC: 2552 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	3.2
DANN	Benign	0.89
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs4245843; hg19: chr2-137039784;