rs543864

chr8-37138389-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 0.607 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/exons	MANE	UniProt

Ensembl

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