chr9-32870070-G-T

Variant names:

• chr9-32870070-G-T
• rs10971170

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 0.0322 in 152,152 control chromosomes in the GnomAD database, including 172 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 0.032 (172 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700

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 = 0.174 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: 0.0322 AC: 4893 AN: 152034 Hom.: 171 Cov.: 31

Gnomad AFR AF: 0.00843

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.0265

Gnomad ASJ AF: 0.0680

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0188

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0292

Gnomad OTH AF: 0.0412

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

GnomAD4 genome AF: 0.0322 AC: 4895 AN: 152152 Hom.: 172 Cov.: 31 AF XY: 0.0341 AC XY: 2536 AN XY: 74370

Gnomad4 AFR AF: 0.00843

Gnomad4 AMR AF: 0.0264

Gnomad4 ASJ AF: 0.0680

Gnomad4 EAS AF: 0.184

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.0188

Gnomad4 NFE AF: 0.0292

Gnomad4 OTH AF: 0.0450

Alfa AF: 0.0266 Hom.: 15

Bravo AF: 0.0314

Asia WGS AF: 0.141 AC: 489 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	1.4
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10971170; hg19: chr9-32870068;