rs6450415

Variant names:

• chr5-57053058-T-C
• rs6450415

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 0.505 in 151,970 control chromosomes in the GnomAD database, including 20,082 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 0.51 (20082 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.510

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.564 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: 0.505 AC: 76742 AN: 151852 Hom.: 20082 Cov.: 32

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.505 AC: 76774 AN: 151970 Hom.: 20082 Cov.: 32 AF XY: 0.503 AC XY: 37389 AN XY: 74294

Gnomad4 AFR AF: 0.413

Gnomad4 AMR AF: 0.534

Gnomad4 ASJ AF: 0.612

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.494

Gnomad4 FIN AF: 0.535

Gnomad4 NFE AF: 0.569

Gnomad4 OTH AF: 0.518

Alfa AF: 0.535 Hom.: 2721

Bravo AF: 0.495

Asia WGS AF: 0.354 AC: 1231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.8
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: rs6450415; hg19: chr5-56348885;