rs10969197

Variant names:

• chr9-29473784-A-G
• rs10969197

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 0.0342 in 152,242 control chromosomes in the GnomAD database, including 119 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 0.034 (119 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.830

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0768 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: 0.0342 AC: 5197 AN: 152124 Hom.: 116 Cov.: 33

Gnomad AFR AF: 0.0319

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.0298

Gnomad ASJ AF: 0.0254

Gnomad EAS AF: 0.0835

Gnomad SAS AF: 0.0265

Gnomad FIN AF: 0.0218

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0343

Gnomad OTH AF: 0.0297

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

GnomAD4 genome AF: 0.0342 AC: 5211 AN: 152242 Hom.: 119 Cov.: 33 AF XY: 0.0334 AC XY: 2485 AN XY: 74428

Gnomad4 AFR AF: 0.0321

Gnomad4 AMR AF: 0.0299

Gnomad4 ASJ AF: 0.0254

Gnomad4 EAS AF: 0.0833

Gnomad4 SAS AF: 0.0269

Gnomad4 FIN AF: 0.0218

Gnomad4 NFE AF: 0.0343

Gnomad4 OTH AF: 0.0294

Alfa AF: 0.0341 Hom.: 143

Bravo AF: 0.0369

Asia WGS AF: 0.0440 AC: 154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.4
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10969197; hg19: chr9-29473782; COSMIC: COSV69457388;