rs10979103

Variant names:

• chr9-107921335-A-G
• rs10979103

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 0.0641 in 152,254 control chromosomes in the GnomAD database, including 413 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 0.064 (413 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460

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 (EAS) allele frequency at 95% confidence interval = 0.137 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: 0.0641 AC: 9748 AN: 152136 Hom.: 412 Cov.: 33

Gnomad AFR AF: 0.0159

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.0478

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.0502

Gnomad FIN AF: 0.0946

Gnomad MID AF: 0.0892

Gnomad NFE AF: 0.0708

Gnomad OTH AF: 0.0690

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

GnomAD4 genome AF: 0.0641 AC: 9754 AN: 152254 Hom.: 413 Cov.: 33 AF XY: 0.0666 AC XY: 4954 AN XY: 74428

Gnomad4 AFR AF: 0.0158

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.0478

Gnomad4 EAS AF: 0.146

Gnomad4 SAS AF: 0.0500

Gnomad4 FIN AF: 0.0946

Gnomad4 NFE AF: 0.0708

Gnomad4 OTH AF: 0.0707

Alfa AF: 0.0640 Hom.: 54

Bravo AF: 0.0650

Asia WGS AF: 0.0980 AC: 342 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	2.0
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10979103; hg19: chr9-110683616;