5-75785095-G-T

Variant names:

• chr5-75785095-G-T
• rs258506

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 0.301 in 151,872 control chromosomes in the GnomAD database, including 7,588 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 0.30 (7588 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.48 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: 0.301 AC: 45670 AN: 151754 Hom.: 7584 Cov.: 32

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.301 AC: 45692 AN: 151872 Hom.: 7588 Cov.: 32 AF XY: 0.304 AC XY: 22546 AN XY: 74234

Gnomad4 AFR AF: 0.159

Gnomad4 AMR AF: 0.285

Gnomad4 ASJ AF: 0.269

Gnomad4 EAS AF: 0.496

Gnomad4 SAS AF: 0.298

Gnomad4 FIN AF: 0.389

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.300

Alfa AF: 0.207 Hom.: 513

Bravo AF: 0.286

Asia WGS AF: 0.359 AC: 1243 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.78
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs258506; hg19: chr5-75080920;