9-113034273-G-T

Variant names:

• chr9-113034273-G-T
• rs10981613

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 0.0602 in 152,148 control chromosomes in the GnomAD database, including 308 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 0.060 (308 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0829 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: 0.0602 AC: 9150 AN: 152030 Hom.: 308 Cov.: 32

Gnomad AFR AF: 0.0666

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0493

Gnomad ASJ AF: 0.0519

Gnomad EAS AF: 0.0776

Gnomad SAS AF: 0.0900

Gnomad FIN AF: 0.0440

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.0582

Gnomad OTH AF: 0.0679

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

GnomAD4 genome AF: 0.0602 AC: 9157 AN: 152148 Hom.: 308 Cov.: 32 AF XY: 0.0609 AC XY: 4531 AN XY: 74368

African (AFR) AF: 0.0668 AC: 2774 AN: 41510

American (AMR) AF: 0.0493 AC: 753 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0519 AC: 180 AN: 3470

East Asian (EAS) AF: 0.0776 AC: 402 AN: 5180

South Asian (SAS) AF: 0.0899 AC: 432 AN: 4808

European-Finnish (FIN) AF: 0.0440 AC: 466 AN: 10602

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.0582 AC: 3959 AN: 68000

Other (OTH) AF: 0.0668 AC: 141 AN: 2112

Alfa AF: 0.0589 Hom.: 535

Bravo AF: 0.0596

Asia WGS AF: 0.0670 AC: 234 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.6
DANN	Benign	0.76
PhyloP100		0.079

Splicing

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

Other links and lift over

dbSNP: rs10981613; hg19: chr9-115796553;