rs4482740

Variant names:

• chr4-154525153-G-A
• rs4482740

Your query was ambiguous. Multiple possible variants found:

• chr4-154525153-G-A
• chr4-154525153-G-C
• chr4-154525153-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 0.321 in 151,872 control chromosomes in the GnomAD database, including 8,217 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 0.32 (8217 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.398 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: 0.321 AC: 48664 AN: 151754 Hom.: 8208 Cov.: 31

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.321 AC: 48701 AN: 151872 Hom.: 8217 Cov.: 31 AF XY: 0.321 AC XY: 23788 AN XY: 74184

African (AFR) AF: 0.219 AC: 9055 AN: 41406

American (AMR) AF: 0.407 AC: 6205 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 970 AN: 3470

East Asian (EAS) AF: 0.294 AC: 1518 AN: 5162

South Asian (SAS) AF: 0.291 AC: 1398 AN: 4800

European-Finnish (FIN) AF: 0.369 AC: 3881 AN: 10508

Middle Eastern (MID) AF: 0.356 AC: 104 AN: 292

European-Non Finnish (NFE) AF: 0.360 AC: 24485 AN: 67950

Other (OTH) AF: 0.332 AC: 700 AN: 2108

Alfa AF: 0.345 Hom.: 15413

Bravo AF: 0.321

Asia WGS AF: 0.295 AC: 1027 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.1
DANN	Benign	0.55
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs4482740; hg19: chr4-155446305;