rs2572357

chr4-48976224-T-G

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/exons	MANE	UniProt

Ensembl

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