9-103027310-G-C

Variant names:

• chr9-103027310-G-C
• rs1417706

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 0.551 in 152,014 control chromosomes in the GnomAD database, including 24,525 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 0.55 (24525 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.220
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.551 AC: 83727 AN: 151896 Hom.: 24478 Cov.: 33

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.807

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.571

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

GnomAD4 genome AF: 0.551 AC: 83826 AN: 152014 Hom.: 24525 Cov.: 33 AF XY: 0.555 AC XY: 41215 AN XY: 74280

African (AFR) AF: 0.637 AC: 26428 AN: 41486

American (AMR) AF: 0.661 AC: 10088 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1744 AN: 3470

East Asian (EAS) AF: 0.889 AC: 4602 AN: 5176

South Asian (SAS) AF: 0.806 AC: 3892 AN: 4826

European-Finnish (FIN) AF: 0.317 AC: 3331 AN: 10520

Middle Eastern (MID) AF: 0.572 AC: 167 AN: 292

European-Non Finnish (NFE) AF: 0.469 AC: 31908 AN: 67972

Other (OTH) AF: 0.576 AC: 1213 AN: 2106

Alfa AF: 0.494 Hom.: 2339

Bravo AF: 0.581

Asia WGS AF: 0.843 AC: 2928 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.7
DANN	Benign	0.30
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs1417706; hg19: chr9-105789592;