rs258748

chr5-143276889-C-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 0.148 in 152,150 control chromosomes in the GnomAD database, including 1,850 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 0.15 (1850 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.723

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.173 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: 0.148 AC: 22543 AN: 152032 Hom.: 1846 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.0825

Gnomad ASJ AF: 0.0623

Gnomad EAS AF: 0.0719

Gnomad SAS AF: 0.0333

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.148 AC: 22577 AN: 152150 Hom.: 1850 Cov.: 32 AF XY: 0.146 AC XY: 10894 AN XY: 74362

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.0824

Gnomad4 ASJ AF: 0.0623

Gnomad4 EAS AF: 0.0719

Gnomad4 SAS AF: 0.0323

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.119

Alfa AF: 0.160 Hom.: 274

Bravo AF: 0.141

Asia WGS AF: 0.0730 AC: 255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
Cadd	Benign	7.9
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs258748; hg19: chr5-142656454;