9-103874297-T-G

Variant names:

• chr9-103874297-T-G
• rs10512320

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.630

Gnomad4 AMR AF: 0.535

Gnomad4 ASJ AF: 0.636

Gnomad4 EAS AF: 0.504

Gnomad4 SAS AF: 0.643

Gnomad4 FIN AF: 0.729

Gnomad4 NFE AF: 0.656

Gnomad4 OTH AF: 0.618

Alfa AF: 0.656 Hom.: 4641

Bravo AF: 0.617

Asia WGS AF: 0.593 AC: 2055 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10512320; hg19: chr9-106636578;