rs10115383

Variant names:

• chr9-100608250-A-G
• rs10115383

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.643 AC: 26661 AN: 41468

American (AMR) AF: 0.725 AC: 11084 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.663 AC: 2301 AN: 3470

East Asian (EAS) AF: 0.651 AC: 3355 AN: 5152

South Asian (SAS) AF: 0.644 AC: 3102 AN: 4820

European-Finnish (FIN) AF: 0.739 AC: 7816 AN: 10578

Middle Eastern (MID) AF: 0.586 AC: 171 AN: 292

European-Non Finnish (NFE) AF: 0.720 AC: 48947 AN: 67988

Other (OTH) AF: 0.686 AC: 1448 AN: 2112

Alfa AF: 0.708 Hom.: 71992

Bravo AF: 0.696

Asia WGS AF: 0.669 AC: 2327 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.2
DANN	Benign	0.83
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs10115383; hg19: chr9-103370532;