rs9322729

Variant names:

• chr6-103463699-T-A
• rs9322729

Your query was ambiguous. Multiple possible variants found:

• chr6-103463699-T-A
• chr6-103463699-T-C

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 0.317 in 151,752 control chromosomes in the GnomAD database, including 8,332 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 0.32 (8332 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.400

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.457 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: 0.317 AC: 48051 AN: 151634 Hom.: 8294 Cov.: 32

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.317 AC: 48140 AN: 151752 Hom.: 8332 Cov.: 32 AF XY: 0.319 AC XY: 23634 AN XY: 74162

Gnomad4 AFR AF: 0.463

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.353

Gnomad4 SAS AF: 0.205

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.244

Gnomad4 OTH AF: 0.274

Alfa AF: 0.134 Hom.: 230

Bravo AF: 0.334

Asia WGS AF: 0.314 AC: 1093 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	5.2
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9322729; hg19: chr6-103911574;