rs6571064

chr6-102846145-A-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 0.0917 in 151,838 control chromosomes in the GnomAD database, including 872 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 0.092 (872 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.409

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.176 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: 0.0917 AC: 13914 AN: 151720 Hom.: 872 Cov.: 32

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.0649

Gnomad ASJ AF: 0.0712

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0280

Gnomad FIN AF: 0.0489

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0641

Gnomad OTH AF: 0.0821

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

GnomAD4 genome AF: 0.0917 AC: 13930 AN: 151838 Hom.: 872 Cov.: 32 AF XY: 0.0879 AC XY: 6530 AN XY: 74252

Gnomad4 AFR AF: 0.180

Gnomad4 AMR AF: 0.0649

Gnomad4 ASJ AF: 0.0712

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0276

Gnomad4 FIN AF: 0.0489

Gnomad4 NFE AF: 0.0641

Gnomad4 OTH AF: 0.0813

Alfa AF: 0.0718 Hom.: 278

Bravo AF: 0.0960

Asia WGS AF: 0.0230 AC: 81 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	4.1
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6571064; hg19: chr6-103294020;