rs2330572

Variant names:

• chr5-44740887-A-C
• rs2330572

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 0.464 in 151,828 control chromosomes in the GnomAD database, including 16,885 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 0.46 (16885 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.591

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.552 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: 0.464 AC: 70420 AN: 151708 Hom.: 16842 Cov.: 32

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.464 AC: 70516 AN: 151828 Hom.: 16885 Cov.: 32 AF XY: 0.467 AC XY: 34629 AN XY: 74162

Gnomad4 AFR AF: 0.558

Gnomad4 AMR AF: 0.475

Gnomad4 ASJ AF: 0.432

Gnomad4 EAS AF: 0.556

Gnomad4 SAS AF: 0.485

Gnomad4 FIN AF: 0.399

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.459

Alfa AF: 0.429 Hom.: 9468

Bravo AF: 0.475

Asia WGS AF: 0.561 AC: 1945 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2330572; hg19: chr5-44740989;