rs10969375

Positions:

• chr9-29783991-T-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;