rs6559140

chr8-6295398-T-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 0.192 in 152,078 control chromosomes in the GnomAD database, including 3,010 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 0.19 (3010 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.508

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.212 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: 0.192 AC: 29188 AN: 151960 Hom.: 3008 Cov.: 33

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.192 AC: 29197 AN: 152078 Hom.: 3010 Cov.: 33 AF XY: 0.191 AC XY: 14201 AN XY: 74346

Gnomad4 AFR AF: 0.189

Gnomad4 AMR AF: 0.140

Gnomad4 ASJ AF: 0.291

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.137

Gnomad4 FIN AF: 0.220

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.198

Alfa AF: 0.212 Hom.: 458

Bravo AF: 0.187

Asia WGS AF: 0.0640 AC: 222 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.44
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6559140; hg19: chr8-6152919;