6-99107880-A-G

Position:

• chr6-99107880-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 0.592 in 152,004 control chromosomes in the GnomAD database, including 26,854 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 0.59 (26854 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.72

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.592 AC: 89892 AN: 151888 Hom.: 26830 Cov.: 32

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.628

Gnomad SAS AF: 0.618

Gnomad FIN AF: 0.642

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.592 AC: 89966 AN: 152004 Hom.: 26854 Cov.: 32 AF XY: 0.594 AC XY: 44099 AN XY: 74296

Gnomad4 AFR AF: 0.552

Gnomad4 AMR AF: 0.550

Gnomad4 ASJ AF: 0.593

Gnomad4 EAS AF: 0.629

Gnomad4 SAS AF: 0.618

Gnomad4 FIN AF: 0.642

Gnomad4 NFE AF: 0.611

Gnomad4 OTH AF: 0.610

Alfa AF: 0.603 Hom.: 15692

Bravo AF: 0.583

Asia WGS AF: 0.659 AC: 2293 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.14
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6905786; hg19: chr6-99555756;