rs2572357

Variant names:

• chr4-48976224-T-G
• rs2572357

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 0.582 in 151,944 control chromosomes in the GnomAD database, including 29,190 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 0.58 (29190 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.182

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.735 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: 0.582 AC: 88350 AN: 151826 Hom.: 29181 Cov.: 31

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.740

Gnomad AMR AF: 0.746

Gnomad ASJ AF: 0.787

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.742

Gnomad MID AF: 0.768

Gnomad NFE AF: 0.722

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.582 AC: 88383 AN: 151944 Hom.: 29190 Cov.: 31 AF XY: 0.583 AC XY: 43327 AN XY: 74262

Gnomad4 AFR AF: 0.266

Gnomad4 AMR AF: 0.746

Gnomad4 ASJ AF: 0.787

Gnomad4 EAS AF: 0.294

Gnomad4 SAS AF: 0.533

Gnomad4 FIN AF: 0.742

Gnomad4 NFE AF: 0.722

Gnomad4 OTH AF: 0.634

Alfa AF: 0.642 Hom.: 5472

Bravo AF: 0.572

Asia WGS AF: 0.445 AC: 1552 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.5
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2572357; hg19: chr4-48978241;