rs562843

Variant names:

• chr8-26870301-T-G
• rs562843

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 0.91 in 152,212 control chromosomes in the GnomAD database, including 63,240 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 0.91 (63240 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.949 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: 0.910 AC: 138387 AN: 152094 Hom.: 63204 Cov.: 31

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.982

Gnomad AMR AF: 0.891

Gnomad ASJ AF: 0.989

Gnomad EAS AF: 0.909

Gnomad SAS AF: 0.931

Gnomad FIN AF: 0.942

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.955

Gnomad OTH AF: 0.912

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

GnomAD4 genome AF: 0.910 AC: 138477 AN: 152212 Hom.: 63240 Cov.: 31 AF XY: 0.910 AC XY: 67751 AN XY: 74414

Gnomad4 AFR AF: 0.823

Gnomad4 AMR AF: 0.890

Gnomad4 ASJ AF: 0.989

Gnomad4 EAS AF: 0.909

Gnomad4 SAS AF: 0.932

Gnomad4 FIN AF: 0.942

Gnomad4 NFE AF: 0.955

Gnomad4 OTH AF: 0.907

Alfa AF: 0.930 Hom.: 8198

Bravo AF: 0.902

Asia WGS AF: 0.898 AC: 3125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.3
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs562843; hg19: chr8-26727818;