chr4-26502361-G-A

Variant names:

• chr4-26502361-G-A
• rs2046784

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 0.432 in 151,910 control chromosomes in the GnomAD database, including 15,325 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 0.43 (15325 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.487
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.611 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: 0.432 AC: 65581 AN: 151792 Hom.: 15292 Cov.: 31

Gnomad AFR AF: 0.617

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.432 AC: 65670 AN: 151910 Hom.: 15325 Cov.: 31 AF XY: 0.430 AC XY: 31903 AN XY: 74232

African (AFR) AF: 0.617 AC: 25570 AN: 41414

American (AMR) AF: 0.358 AC: 5464 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1565 AN: 3468

East Asian (EAS) AF: 0.509 AC: 2631 AN: 5168

South Asian (SAS) AF: 0.541 AC: 2595 AN: 4794

European-Finnish (FIN) AF: 0.295 AC: 3112 AN: 10540

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.346 AC: 23480 AN: 67942

Other (OTH) AF: 0.425 AC: 894 AN: 2106

Alfa AF: 0.397 Hom.: 2220

Bravo AF: 0.446

Asia WGS AF: 0.544 AC: 1889 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.28
DANN	Benign	0.44
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs2046784; hg19: chr4-26503983;