rs543864

Variant names:

• chr8-37138389-G-A
• rs543864

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 0.607 in 152,068 control chromosomes in the GnomAD database, including 30,400 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 0.61 (30400 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.708 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: 0.608 AC: 92327 AN: 151950 Hom.: 30403 Cov.: 32

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.727

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.683

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.726

Gnomad FIN AF: 0.804

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.618

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

GnomAD4 genome AF: 0.607 AC: 92367 AN: 152068 Hom.: 30400 Cov.: 32 AF XY: 0.614 AC XY: 45647 AN XY: 74330

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.704

Gnomad4 ASJ AF: 0.683

Gnomad4 EAS AF: 0.492

Gnomad4 SAS AF: 0.727

Gnomad4 FIN AF: 0.804

Gnomad4 NFE AF: 0.713

Gnomad4 OTH AF: 0.614

Alfa AF: 0.642 Hom.: 8482

Bravo AF: 0.588

Asia WGS AF: 0.575 AC: 2002 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.015
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs543864; hg19: chr8-36995907;