rs9376092

Variant names:

• chr6-135106006-C-A
• rs9376092

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 0.244 in 151,960 control chromosomes in the GnomAD database, including 4,840 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 0.24 (4840 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0920

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• 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: 0.244 AC: 37060 AN: 151842 Hom.: 4834 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.244 AC: 37074 AN: 151960 Hom.: 4840 Cov.: 32 AF XY: 0.243 AC XY: 18056 AN XY: 74236

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.237

Gnomad4 EAS AF: 0.280

Gnomad4 SAS AF: 0.111

Gnomad4 FIN AF: 0.349

Gnomad4 NFE AF: 0.270

Gnomad4 OTH AF: 0.218

Alfa AF: 0.262 Hom.: 12209

Bravo AF: 0.237

Asia WGS AF: 0.178 AC: 619 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.0
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9376092; hg19: chr6-135427144; COSMIC: COSV73231457;