6-98563625-A-G

Variant names:

• chr6-98563625-A-G
• rs2086512

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 0.824 in 152,088 control chromosomes in the GnomAD database, including 52,693 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 0.82 (52693 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.893 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: 0.825 AC: 125323 AN: 151970 Hom.: 52668 Cov.: 31

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.859

Gnomad AMR AF: 0.893

Gnomad ASJ AF: 0.822

Gnomad EAS AF: 0.914

Gnomad SAS AF: 0.846

Gnomad FIN AF: 0.950

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.890

Gnomad OTH AF: 0.833

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

GnomAD4 genome AF: 0.824 AC: 125392 AN: 152088 Hom.: 52693 Cov.: 31 AF XY: 0.827 AC XY: 61536 AN XY: 74364

African (AFR) AF: 0.644 AC: 26686 AN: 41450

American (AMR) AF: 0.893 AC: 13660 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.822 AC: 2850 AN: 3466

East Asian (EAS) AF: 0.915 AC: 4717 AN: 5156

South Asian (SAS) AF: 0.846 AC: 4071 AN: 4810

European-Finnish (FIN) AF: 0.950 AC: 10068 AN: 10596

Middle Eastern (MID) AF: 0.871 AC: 256 AN: 294

European-Non Finnish (NFE) AF: 0.890 AC: 60548 AN: 68002

Other (OTH) AF: 0.832 AC: 1753 AN: 2108

Alfa AF: 0.862 Hom.: 135871

Bravo AF: 0.812

Asia WGS AF: 0.857 AC: 2982 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	9.2
DANN	Benign	0.65
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs2086512; hg19: chr6-99011501;