9-6172380-A-G

Variant names:

• chr9-6172380-A-G
• rs7032572

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 0.146 in 152,184 control chromosomes in the GnomAD database, including 1,768 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 0.15 (1768 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

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 (NFE) allele frequency at 95% confidence interval = 0.16 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: 0.146 AC: 22187 AN: 152066 Hom.: 1770 Cov.: 31

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.146 AC: 22197 AN: 152184 Hom.: 1768 Cov.: 31 AF XY: 0.147 AC XY: 10934 AN XY: 74418

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.158

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.162

Gnomad4 OTH AF: 0.150

Alfa AF: 0.137 Hom.: 854

Bravo AF: 0.144

Asia WGS AF: 0.0660 AC: 231 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	3.9
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7032572; hg19: chr9-6172380;