rs1482113

Variant names:

• chr4-52228301-G-A
• rs1482113

Your query was ambiguous. Multiple possible variants found:

• chr4-52228301-G-A
• chr4-52228301-G-C
• chr4-52228301-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 0.848 in 152,138 control chromosomes in the GnomAD database, including 58,567 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 0.85 (58567 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.361
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.99 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: 0.848 AC: 128954 AN: 152020 Hom.: 58535 Cov.: 32

Gnomad AFR AF: 0.484

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.929

Gnomad ASJ AF: 0.980

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.989

Gnomad FIN AF: 0.999

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.996

Gnomad OTH AF: 0.881

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

GnomAD4 genome AF: 0.848 AC: 129042 AN: 152138 Hom.: 58567 Cov.: 32 AF XY: 0.853 AC XY: 63474 AN XY: 74386

African (AFR) AF: 0.485 AC: 20083 AN: 41422

American (AMR) AF: 0.929 AC: 14200 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.980 AC: 3399 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5187 AN: 5188

South Asian (SAS) AF: 0.990 AC: 4778 AN: 4828

European-Finnish (FIN) AF: 0.999 AC: 10605 AN: 10620

Middle Eastern (MID) AF: 0.935 AC: 275 AN: 294

European-Non Finnish (NFE) AF: 0.996 AC: 67741 AN: 68014

Other (OTH) AF: 0.882 AC: 1862 AN: 2110

Alfa AF: 0.926 Hom.: 24155

Bravo AF: 0.827

Asia WGS AF: 0.964 AC: 3355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.4
DANN	Benign	0.70
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs1482113; hg19: chr4-53094467;