rs9391709

Variant names:

• chr6-31109628-G-C
• rs9391709

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0148 AC: 617 AN: 41594

American (AMR) AF: 0.0889 AC: 1359 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0449 AC: 156 AN: 3472

East Asian (EAS) AF: 0.214 AC: 1107 AN: 5180

South Asian (SAS) AF: 0.133 AC: 644 AN: 4832

European-Finnish (FIN) AF: 0.0882 AC: 936 AN: 10612

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0752 AC: 5117 AN: 68022

Other (OTH) AF: 0.0747 AC: 158 AN: 2114

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
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs9391709; hg19: chr6-31077405;