chr6-85170898-A-G

Variant names:

• chr6-85170898-A-G
• rs1570933

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 0.568 in 152,074 control chromosomes in the GnomAD database, including 25,590 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 0.57 (25590 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.280
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.919 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86307 AN: 151956 Hom.: 25579 Cov.: 32

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.942

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.568 AC: 86368 AN: 152074 Hom.: 25590 Cov.: 32 AF XY: 0.578 AC XY: 43008 AN XY: 74364

African (AFR) AF: 0.640 AC: 26544 AN: 41474

American (AMR) AF: 0.638 AC: 9756 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.523 AC: 1814 AN: 3470

East Asian (EAS) AF: 0.941 AC: 4869 AN: 5172

South Asian (SAS) AF: 0.685 AC: 3300 AN: 4818

European-Finnish (FIN) AF: 0.582 AC: 6155 AN: 10578

Middle Eastern (MID) AF: 0.459 AC: 134 AN: 292

European-Non Finnish (NFE) AF: 0.474 AC: 32242 AN: 67954

Other (OTH) AF: 0.531 AC: 1123 AN: 2116

Alfa AF: 0.505 Hom.: 44664

Bravo AF: 0.576

Asia WGS AF: 0.782 AC: 2716 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.7
DANN	Benign	0.63
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs1570933; hg19: chr6-85880616;