rs2046784

chr4-26502361-G-Achr4-26502361-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;