rs1420846

Variant names:

• chr8-5278271-G-A
• rs1420846

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 0.856 in 152,242 control chromosomes in the GnomAD database, including 55,929 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 0.86 (55929 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.571

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.897 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: 0.856 AC: 130243 AN: 152124 Hom.: 55896 Cov.: 34

Gnomad AFR AF: 0.794

Gnomad AMI AF: 0.944

Gnomad AMR AF: 0.905

Gnomad ASJ AF: 0.831

Gnomad EAS AF: 0.918

Gnomad SAS AF: 0.919

Gnomad FIN AF: 0.864

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.872

Gnomad OTH AF: 0.871

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

GnomAD4 genome AF: 0.856 AC: 130332 AN: 152242 Hom.: 55929 Cov.: 34 AF XY: 0.858 AC XY: 63871 AN XY: 74436

Gnomad4 AFR AF: 0.794

Gnomad4 AMR AF: 0.906

Gnomad4 ASJ AF: 0.831

Gnomad4 EAS AF: 0.918

Gnomad4 SAS AF: 0.919

Gnomad4 FIN AF: 0.864

Gnomad4 NFE AF: 0.872

Gnomad4 OTH AF: 0.868

Alfa AF: 0.864 Hom.: 17553

Bravo AF: 0.857

Asia WGS AF: 0.900 AC: 3130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.24
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1420846; hg19: chr8-5135793;