6-99107880-A-G

Variant names:

• chr6-99107880-A-G
• rs6905786

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;