rs10979103

Positions:

• chr9-107921335-A-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;