chr6-131900566-A-G

Variant names:

• chr6-131900566-A-G
• rs9373000

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 0.302 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.302 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

Gnomad4 AFR AF: 0.358

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.325

Gnomad4 EAS AF: 0.278

Gnomad4 SAS AF: 0.451

Gnomad4 FIN AF: 0.334

Gnomad4 NFE AF: 0.249

Gnomad4 OTH AF: 0.309

Alfa AF: 0.273 Hom.: 2663

Bravo AF: 0.299

Asia WGS AF: 0.390 AC: 1358 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9373000; hg19: chr6-132221706;