rs2330572

Positions:

• chr5-44740887-A-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 0.464 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/exons	MANE	UniProt

Ensembl

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