rs2433320

chr4-94449654-G-A

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 0.365 in 151,490 control chromosomes in the GnomAD database, including 10,674 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 0.36 (10674 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.437 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: 0.365 AC: 55209 AN: 151370 Hom.: 10671 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.365 AC: 55233 AN: 151490 Hom.: 10674 Cov.: 32 AF XY: 0.358 AC XY: 26511 AN XY: 74028

Gnomad4 AFR AF: 0.274

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.410

Gnomad4 EAS AF: 0.185

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.400

Gnomad4 NFE AF: 0.441

Gnomad4 OTH AF: 0.406

Alfa AF: 0.417 Hom.: 28321

Bravo AF: 0.352

Asia WGS AF: 0.187 AC: 649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.46
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2433320; hg19: chr4-95370805;