rs9390939

Variant names:

• chr6-103036537-A-C
• rs9390939

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 0.267 in 151,886 control chromosomes in the GnomAD database, including 5,791 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 0.27 (5791 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.679

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 (NFE) allele frequency at 95% confidence interval = 0.308 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: 0.267 AC: 40504 AN: 151768 Hom.: 5794 Cov.: 32

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.267 AC: 40503 AN: 151886 Hom.: 5791 Cov.: 32 AF XY: 0.265 AC XY: 19704 AN XY: 74236

Gnomad4 AFR AF: 0.180

Gnomad4 AMR AF: 0.290

Gnomad4 ASJ AF: 0.488

Gnomad4 EAS AF: 0.270

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.209

Gnomad4 NFE AF: 0.311

Gnomad4 OTH AF: 0.299

Alfa AF: 0.305 Hom.: 14699

Bravo AF: 0.269

Asia WGS AF: 0.228 AC: 791 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	4.4
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9390939; hg19: chr6-103484412;