9-103874297-T-G

Variant names:

• chr9-103874297-T-G
• rs10512320

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 0.635 in 152,002 control chromosomes in the GnomAD database, including 30,883 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 0.64 (30883 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.651 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: 0.635 AC: 96467 AN: 151884 Hom.: 30866 Cov.: 32

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.656

Gnomad OTH AF: 0.624

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

GnomAD4 genome AF: 0.635 AC: 96528 AN: 152002 Hom.: 30883 Cov.: 32 AF XY: 0.637 AC XY: 47354 AN XY: 74302

African (AFR) AF: 0.630 AC: 26103 AN: 41438

American (AMR) AF: 0.535 AC: 8171 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.636 AC: 2207 AN: 3470

East Asian (EAS) AF: 0.504 AC: 2606 AN: 5168

South Asian (SAS) AF: 0.643 AC: 3092 AN: 4808

European-Finnish (FIN) AF: 0.729 AC: 7710 AN: 10576

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.656 AC: 44617 AN: 67966

Other (OTH) AF: 0.618 AC: 1303 AN: 2108

Alfa AF: 0.655 Hom.: 4794

Bravo AF: 0.617

Asia WGS AF: 0.593 AC: 2055 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	7.3
DANN	Benign	0.74
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs10512320; hg19: chr9-106636578;