rs9391709

chr6-31109628-G-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 0.0667 in 152,322 control chromosomes in the GnomAD database, including 510 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 0.067 (510 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.307

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.203 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: 0.0668 AC: 10171 AN: 152204 Hom.: 514 Cov.: 32

Gnomad AFR AF: 0.0148

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0894

Gnomad ASJ AF: 0.0449

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.0882

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0752

Gnomad OTH AF: 0.0750

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

GnomAD4 genome AF: 0.0667 AC: 10156 AN: 152322 Hom.: 510 Cov.: 32 AF XY: 0.0694 AC XY: 5166 AN XY: 74490

Gnomad4 AFR AF: 0.0148

Gnomad4 AMR AF: 0.0889

Gnomad4 ASJ AF: 0.0449

Gnomad4 EAS AF: 0.214

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.0882

Gnomad4 NFE AF: 0.0752

Gnomad4 OTH AF: 0.0747

Alfa AF: 0.0654 Hom.: 52

Bravo AF: 0.0633

Asia WGS AF: 0.138 AC: 479 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	4.3
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9391709; hg19: chr6-31077405;