9-30816507-T-G

Variant names:

• chr9-30816507-T-G
• rs10511868

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 0.0392 in 152,290 control chromosomes in the GnomAD database, including 293 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 0.039 (293 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.631

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.255 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: 0.0392 AC: 5972 AN: 152172 Hom.: 293 Cov.: 32

Gnomad AFR AF: 0.0376

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0473

Gnomad ASJ AF: 0.0124

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.0275

Gnomad FIN AF: 0.0797

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0178

Gnomad OTH AF: 0.0349

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

GnomAD4 genome AF: 0.0392 AC: 5972 AN: 152290 Hom.: 293 Cov.: 32 AF XY: 0.0424 AC XY: 3156 AN XY: 74460

Gnomad4 AFR AF: 0.0375

Gnomad4 AMR AF: 0.0475

Gnomad4 ASJ AF: 0.0124

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.0273

Gnomad4 FIN AF: 0.0797

Gnomad4 NFE AF: 0.0178

Gnomad4 OTH AF: 0.0336

Alfa AF: 0.0236 Hom.: 17

Bravo AF: 0.0411

Asia WGS AF: 0.141 AC: 488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10511868; hg19: chr9-30816505;