rs2046784

Variant names:

• chr4-26502361-G-A
• rs2046784

Your query was ambiguous. Multiple possible variants found:

• chr4-26502361-G-A
• chr4-26502361-G-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.617

Gnomad4 AMR AF: 0.358

Gnomad4 ASJ AF: 0.451

Gnomad4 EAS AF: 0.509

Gnomad4 SAS AF: 0.541

Gnomad4 FIN AF: 0.295

Gnomad4 NFE AF: 0.346

Gnomad4 OTH AF: 0.425

Alfa AF: 0.389 Hom.: 2059

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2046784; hg19: chr4-26503983;