chr5-151167583-C-T

Variant names:

• chr5-151167583-C-T
• rs366307

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 0.499 in 151,924 control chromosomes in the GnomAD database, including 19,478 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 0.50 (19478 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.751

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.625 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: 0.499 AC: 75744 AN: 151806 Hom.: 19468 Cov.: 31

Gnomad AFR AF: 0.632

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.499 AC: 75790 AN: 151924 Hom.: 19478 Cov.: 31 AF XY: 0.493 AC XY: 36615 AN XY: 74238

Gnomad4 AFR AF: 0.631

Gnomad4 AMR AF: 0.454

Gnomad4 ASJ AF: 0.483

Gnomad4 EAS AF: 0.291

Gnomad4 SAS AF: 0.291

Gnomad4 FIN AF: 0.456

Gnomad4 NFE AF: 0.467

Gnomad4 OTH AF: 0.488

Alfa AF: 0.485 Hom.: 3662

Bravo AF: 0.509

Asia WGS AF: 0.327 AC: 1134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs366307; hg19: chr5-150547144;