rs9321490

Variant names:

• chr6-135173737-T-C
• rs9321490

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 0.257 in 152,032 control chromosomes in the GnomAD database, including 5,215 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 0.26 (5215 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.358 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: 0.257 AC: 39055 AN: 151914 Hom.: 5203 Cov.: 31

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.257 AC: 39098 AN: 152032 Hom.: 5215 Cov.: 31 AF XY: 0.261 AC XY: 19425 AN XY: 74320

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.218

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.347

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.230

Gnomad4 OTH AF: 0.272

Alfa AF: 0.239 Hom.: 5068

Bravo AF: 0.259

Asia WGS AF: 0.378 AC: 1313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.11
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9321490; hg19: chr6-135494875;