chr6-106700598-G-C

Variant names:

• chr6-106700598-G-C
• rs2798360

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.859 in 152,238 control chromosomes in the GnomAD database, including 56,295 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 0.86 (56295 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.727
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.859 AC: 130655 AN: 152120 Hom.: 56233 Cov.: 32

Gnomad AFR AF: 0.867

Gnomad AMI AF: 0.867

Gnomad AMR AF: 0.883

Gnomad ASJ AF: 0.934

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.896

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.854

Gnomad OTH AF: 0.855

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

GnomAD4 genome AF: 0.859 AC: 130777 AN: 152238 Hom.: 56295 Cov.: 32 AF XY: 0.859 AC XY: 63932 AN XY: 74426

African (AFR) AF: 0.868 AC: 36029 AN: 41528

American (AMR) AF: 0.884 AC: 13520 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.934 AC: 3242 AN: 3470

East Asian (EAS) AF: 0.745 AC: 3858 AN: 5180

South Asian (SAS) AF: 0.769 AC: 3705 AN: 4820

European-Finnish (FIN) AF: 0.896 AC: 9502 AN: 10606

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.854 AC: 58084 AN: 68016

Other (OTH) AF: 0.857 AC: 1810 AN: 2112

Alfa AF: 0.855 Hom.: 2756

Bravo AF: 0.861

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.83
DANN	Benign	0.43
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs2798360; hg19: chr6-107148473;