rs245061

Variant names:

• chr5-149955992-A-G
• rs245061

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 0.424 in 151,752 control chromosomes in the GnomAD database, including 14,269 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 0.42 (14269 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.489 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: 0.424 AC: 64305 AN: 151634 Hom.: 14270 Cov.: 29

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.424 AC: 64322 AN: 151752 Hom.: 14269 Cov.: 29 AF XY: 0.419 AC XY: 31086 AN XY: 74144

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.360

Gnomad4 ASJ AF: 0.539

Gnomad4 EAS AF: 0.214

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.540

Gnomad4 NFE AF: 0.494

Gnomad4 OTH AF: 0.405

Alfa AF: 0.461 Hom.: 2064

Bravo AF: 0.406

Asia WGS AF: 0.294 AC: 1028 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.33
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs245061; hg19: chr5-149335555;