rs10969375

Variant names:

• chr9-29783991-T-C
• rs10969375

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 0.189 in 152,116 control chromosomes in the GnomAD database, including 2,883 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 0.19 (2883 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.907

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 (AFR) allele frequency at 95% confidence interval = 0.251 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: 0.189 AC: 28698 AN: 151998 Hom.: 2875 Cov.: 32

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.0941

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.0573

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.189 AC: 28734 AN: 152116 Hom.: 2883 Cov.: 32 AF XY: 0.189 AC XY: 14047 AN XY: 74364

Gnomad4 AFR AF: 0.255

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.0941

Gnomad4 EAS AF: 0.134

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.209

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.152

Alfa AF: 0.159 Hom.: 1798

Bravo AF: 0.186

Asia WGS AF: 0.158 AC: 547 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	0.32
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10969375; hg19: chr9-29783989;