rs1458439

Variant names:

• chr6-77534774-C-T
• rs1458439

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 0.616 in 151,650 control chromosomes in the GnomAD database, including 29,206 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 0.62 (29206 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.962

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.835 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: 0.617 AC: 93445 AN: 151532 Hom.: 29207 Cov.: 31

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.856

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.599

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

GnomAD4 genome AF: 0.616 AC: 93475 AN: 151650 Hom.: 29206 Cov.: 31 AF XY: 0.614 AC XY: 45439 AN XY: 74042

Gnomad4 AFR AF: 0.539

Gnomad4 AMR AF: 0.632

Gnomad4 ASJ AF: 0.564

Gnomad4 EAS AF: 0.856

Gnomad4 SAS AF: 0.567

Gnomad4 FIN AF: 0.621

Gnomad4 NFE AF: 0.648

Gnomad4 OTH AF: 0.602

Alfa AF: 0.633 Hom.: 3856

Bravo AF: 0.615

Asia WGS AF: 0.709 AC: 2464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1458439; hg19: chr6-78244491;