rs4416533

Variant names:

• chr4-137405718-G-A
• rs4416533

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 0.553 in 151,606 control chromosomes in the GnomAD database, including 23,792 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 0.55 (23792 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.292
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.675 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: 0.554 AC: 83856 AN: 151488 Hom.: 23793 Cov.: 31

Gnomad AFR AF: 0.682

Gnomad AMI AF: 0.636

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.553 AC: 83889 AN: 151606 Hom.: 23792 Cov.: 31 AF XY: 0.551 AC XY: 40805 AN XY: 74044

African (AFR) AF: 0.681 AC: 28077 AN: 41212

American (AMR) AF: 0.551 AC: 8410 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1615 AN: 3464

East Asian (EAS) AF: 0.486 AC: 2491 AN: 5128

South Asian (SAS) AF: 0.422 AC: 2031 AN: 4808

European-Finnish (FIN) AF: 0.521 AC: 5465 AN: 10486

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.499 AC: 33918 AN: 67942

Other (OTH) AF: 0.530 AC: 1119 AN: 2112

Alfa AF: 0.547 Hom.: 3326

Bravo AF: 0.561

Asia WGS AF: 0.436 AC: 1518 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.36
DANN	Benign	0.53
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs4416533; hg19: chr4-138326872;