6-131900566-A-G

Variant names:

• chr6-131900566-A-G
• rs9373000

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 0.302 in 151,116 control chromosomes in the GnomAD database, including 7,187 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 0.30 (7187 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.843
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.435 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: 0.302 AC: 45666 AN: 151004 Hom.: 7180 Cov.: 30

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.302 AC: 45711 AN: 151116 Hom.: 7187 Cov.: 30 AF XY: 0.312 AC XY: 23013 AN XY: 73780

African (AFR) AF: 0.358 AC: 14675 AN: 41010

American (AMR) AF: 0.328 AC: 4983 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1123 AN: 3458

East Asian (EAS) AF: 0.278 AC: 1418 AN: 5106

South Asian (SAS) AF: 0.451 AC: 2153 AN: 4776

European-Finnish (FIN) AF: 0.334 AC: 3462 AN: 10380

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16879 AN: 67866

Other (OTH) AF: 0.309 AC: 651 AN: 2104

Alfa AF: 0.273 Hom.: 2977

Bravo AF: 0.299

Asia WGS AF: 0.390 AC: 1358 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	2.1
DANN	Benign	0.88
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs9373000; hg19: chr6-132221706;