rs562843

Positions:

• chr8-26870301-T-G

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/exons	MANE	UniProt

Ensembl

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