rs57450513

chr5-141845881-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0151 in 149,184 control chromosomes in the GnomAD database, including 20 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 0.015 (20 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.213

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BS1: Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0151 (2260/149184) while in subpopulation AMR AF= 0.0281 (417/14840). AF 95% confidence interval is 0.0259. There are 20 homozygotes in gnomad4. There are 1079 alleles in male gnomad4 subpopulation. Median coverage is 26. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 20 gene

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: 0.0152 AC: 2262 AN: 149072 Hom.: 20 Cov.: 26

Gnomad AFR AF: 0.00936

Gnomad AMI AF: 0.00554

Gnomad AMR AF: 0.0281

Gnomad ASJ AF: 0.00609

Gnomad EAS AF: 0.000392

Gnomad SAS AF: 0.00522

Gnomad FIN AF: 0.0131

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0183

Gnomad OTH AF: 0.0202

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

GnomAD4 genome AF: 0.0151 AC: 2260 AN: 149184 Hom.: 20 Cov.: 26 AF XY: 0.0148 AC XY: 1079 AN XY: 72766

Gnomad4 AFR AF: 0.00931

Gnomad4 AMR AF: 0.0281

Gnomad4 ASJ AF: 0.00609

Gnomad4 EAS AF: 0.000393

Gnomad4 SAS AF: 0.00501

Gnomad4 FIN AF: 0.0131

Gnomad4 NFE AF: 0.0183

Gnomad4 OTH AF: 0.0199

Alfa AF: 0.0180 Hom.: 2

Asia WGS AF: 0.00375 AC: 13 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	9.7
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs57450513; hg19: chr5-141225446;