rs9389269

Variant names:

• chr6-135106021-T-C
• rs9389269

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 0.206 in 152,124 control chromosomes in the GnomAD database, including 3,974 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 0.21 (3974 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.809

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 = 0.268 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: 0.206 AC: 31303 AN: 152006 Hom.: 3972 Cov.: 32

Gnomad AFR AF: 0.0719

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.206 AC: 31303 AN: 152124 Hom.: 3974 Cov.: 32 AF XY: 0.206 AC XY: 15300 AN XY: 74342

Gnomad4 AFR AF: 0.0718

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.237

Gnomad4 EAS AF: 0.280

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.348

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.183

Alfa AF: 0.248 Hom.: 4676

Bravo AF: 0.192

Asia WGS AF: 0.163 AC: 564 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	0.63
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9389269; hg19: chr6-135427159; COSMIC: COSV73231458;