rs10908907

Variant names:

• chr9-89634669-G-A
• rs10908907

Your query was ambiguous. Multiple possible variants found:

• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;