rs10115383

Variant names:

• chr9-100608250-A-G
• rs10115383

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 0.694 in 152,070 control chromosomes in the GnomAD database, including 36,823 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 0.69 (36823 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.376

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.715 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: 0.694 AC: 105498 AN: 151952 Hom.: 36805 Cov.: 32

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.736

Gnomad AMR AF: 0.725

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.739

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.694 AC: 105556 AN: 152070 Hom.: 36823 Cov.: 32 AF XY: 0.694 AC XY: 51599 AN XY: 74324

Gnomad4 AFR AF: 0.643

Gnomad4 AMR AF: 0.725

Gnomad4 ASJ AF: 0.663

Gnomad4 EAS AF: 0.651

Gnomad4 SAS AF: 0.644

Gnomad4 FIN AF: 0.739

Gnomad4 NFE AF: 0.720

Gnomad4 OTH AF: 0.686

Alfa AF: 0.712 Hom.: 52982

Bravo AF: 0.696

Asia WGS AF: 0.669 AC: 2327 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.2
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10115383; hg19: chr9-103370532;