rs2433320

Variant names:

• chr4-94449654-G-A
• rs2433320

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;