rs10971170

Variant names:

• chr9-32870070-G-T
• rs10971170

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 0.0322 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
• Publications: 2 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 = 0.174 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

African (AFR) AF: 0.00843 AC: 350 AN: 41524

American (AMR) AF: 0.0264 AC: 404 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0680 AC: 236 AN: 3470

East Asian (EAS) AF: 0.184 AC: 946 AN: 5148

South Asian (SAS) AF: 0.101 AC: 487 AN: 4814

European-Finnish (FIN) AF: 0.0188 AC: 199 AN: 10590

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0292 AC: 1986 AN: 68002

Other (OTH) AF: 0.0450 AC: 95 AN: 2110

Alfa AF: 0.0333 Hom.: 255

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
PhyloP100		-0.0070

Splicing

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

Other links and lift over

dbSNP: rs10971170; hg19: chr9-32870068;