rs9389269

chr6-135106021-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 0.206 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;