rs10908907

Positions:

• chr9-89634669-G-A
• chr9-89634669-G-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 0.41 in 151,994 control chromosomes in the GnomAD database, including 14,983 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 0.41 (14983 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62248 AN: 151876 Hom.: 14958 Cov.: 33

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.410 AC: 62323 AN: 151994 Hom.: 14983 Cov.: 33 AF XY: 0.417 AC XY: 30985 AN XY: 74276

Gnomad4 AFR AF: 0.622

Gnomad4 AMR AF: 0.493

Gnomad4 ASJ AF: 0.428

Gnomad4 EAS AF: 0.520

Gnomad4 SAS AF: 0.632

Gnomad4 FIN AF: 0.208

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.412

Alfa AF: 0.316 Hom.: 19064

Bravo AF: 0.440

Asia WGS AF: 0.537 AC: 1867 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.47
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10908907; hg19: chr9-92249584; COSMIC: COSV60376140;