rs9468925

Variant names:

• chr6-31291060-G-A
• rs9468925

Your query was ambiguous. Multiple possible variants found:

• chr6-31291060-G-A
• chr6-31291060-G-C
• chr6-31291060-G-T

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 0.443 in 152,078 control chromosomes in the GnomAD database, including 15,400 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 0.44 (15400 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.422

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.545 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: 0.443 AC: 67272 AN: 151958 Hom.: 15374 Cov.: 32

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.443 AC: 67337 AN: 152078 Hom.: 15400 Cov.: 32 AF XY: 0.449 AC XY: 33335 AN XY: 74310

Gnomad4 AFR AF: 0.551

Gnomad4 AMR AF: 0.479

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.377

Gnomad4 SAS AF: 0.459

Gnomad4 FIN AF: 0.494

Gnomad4 NFE AF: 0.370

Gnomad4 OTH AF: 0.443

Alfa AF: 0.379 Hom.: 15445

Bravo AF: 0.446

Asia WGS AF: 0.430 AC: 1496 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.6
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9468925; hg19: chr6-31258837;