9-103607662-G-A

Variant names:

• chr9-103607662-G-A
• rs144649413

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 0.10 (737 hom., cov: 15)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.102 AC: 12740 AN: 124318 Hom.: 738 Cov.: 15

Gnomad AFR AF: 0.0609

Gnomad AMI AF: 0.0801

Gnomad AMR AF: 0.0944

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.0568

Gnomad FIN AF: 0.0815

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.102 AC: 12743 AN: 124432 Hom.: 737 Cov.: 15 AF XY: 0.100 AC XY: 5946 AN XY: 59272

African (AFR) AF: 0.0608 AC: 1890 AN: 31080

American (AMR) AF: 0.0942 AC: 1082 AN: 11490

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 594 AN: 3120

East Asian (EAS) AF: 0.131 AC: 553 AN: 4208

South Asian (SAS) AF: 0.0573 AC: 213 AN: 3720

European-Finnish (FIN) AF: 0.0815 AC: 646 AN: 7930

Middle Eastern (MID) AF: 0.203 AC: 56 AN: 276

European-Non Finnish (NFE) AF: 0.124 AC: 7460 AN: 60144

Other (OTH) AF: 0.112 AC: 182 AN: 1628

Alfa AF: 0.116 Hom.: 128

Bravo AF: 0.0998

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.0
DANN	Benign	0.79

Splicing

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

Other links and lift over

dbSNP: rs144649413; hg19: chr9-106369944;