rs258747

Variant names:

• chr5-143277248-A-G
• rs258747

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 0.471 in 152,010 control chromosomes in the GnomAD database, including 17,426 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 0.47 (17426 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.532 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: 0.471 AC: 71610 AN: 151892 Hom.: 17412 Cov.: 32

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.471 AC: 71661 AN: 152010 Hom.: 17426 Cov.: 32 AF XY: 0.465 AC XY: 34545 AN XY: 74290

Gnomad4 AFR AF: 0.419

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.475

Gnomad4 EAS AF: 0.276

Gnomad4 SAS AF: 0.392

Gnomad4 FIN AF: 0.502

Gnomad4 NFE AF: 0.537

Gnomad4 OTH AF: 0.461

Alfa AF: 0.514 Hom.: 27404

Bravo AF: 0.461

Asia WGS AF: 0.370 AC: 1290 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.62
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs258747; hg19: chr5-142656813;