rs1420846

Positions:

• chr8-5278271-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;