chr9-97862320-G-C

Variant names:

• chr9-97862320-G-C
• rs10119760

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 0.719 in 152,088 control chromosomes in the GnomAD database, including 40,363 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 0.72 (40363 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.966

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.9 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: 0.718 AC: 109185 AN: 151970 Hom.: 40308 Cov.: 32

Gnomad AFR AF: 0.887

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.691

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.921

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.711

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

GnomAD4 genome AF: 0.719 AC: 109290 AN: 152088 Hom.: 40363 Cov.: 32 AF XY: 0.721 AC XY: 53577 AN XY: 74354

Gnomad4 AFR AF: 0.887

Gnomad4 AMR AF: 0.692

Gnomad4 ASJ AF: 0.636

Gnomad4 EAS AF: 0.921

Gnomad4 SAS AF: 0.675

Gnomad4 FIN AF: 0.647

Gnomad4 NFE AF: 0.629

Gnomad4 OTH AF: 0.710

Alfa AF: 0.574 Hom.: 1754

Bravo AF: 0.731

Asia WGS AF: 0.785 AC: 2733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	0.57
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10119760; hg19: chr9-100624602;