rs9291683

Variant names:

• chr4-10322536-G-A
• rs9291683

Your query was ambiguous. Multiple possible variants found:

• chr4-10322536-G-A
• chr4-10322536-G-C
• chr4-10322536-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 0.426 in 151,976 control chromosomes in the GnomAD database, including 14,098 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 0.43 (14098 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.525 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: 0.427 AC: 64775 AN: 151858 Hom.: 14097 Cov.: 32

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.404

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.426 AC: 64789 AN: 151976 Hom.: 14098 Cov.: 32 AF XY: 0.426 AC XY: 31641 AN XY: 74292

Gnomad4 AFR AF: 0.337

Gnomad4 AMR AF: 0.407

Gnomad4 ASJ AF: 0.483

Gnomad4 EAS AF: 0.293

Gnomad4 SAS AF: 0.542

Gnomad4 FIN AF: 0.460

Gnomad4 NFE AF: 0.477

Gnomad4 OTH AF: 0.449

Alfa AF: 0.464 Hom.: 36381

Bravo AF: 0.418

Asia WGS AF: 0.432 AC: 1500 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.065
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9291683; hg19: chr4-10324160;