9-30796761-T-G

Variant names:

• chr9-30796761-T-G
• rs10511866

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 0.0339 in 152,302 control chromosomes in the GnomAD database, including 259 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 0.034 (259 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.216
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.236 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: 0.0340 AC: 5178 AN: 152182 Hom.: 260 Cov.: 32

Gnomad AFR AF: 0.00678

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0331

Gnomad ASJ AF: 0.0311

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.0433

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0286

Gnomad OTH AF: 0.0306

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

GnomAD4 genome AF: 0.0339 AC: 5167 AN: 152302 Hom.: 259 Cov.: 32 AF XY: 0.0360 AC XY: 2683 AN XY: 74484

African (AFR) AF: 0.00676 AC: 281 AN: 41578

American (AMR) AF: 0.0330 AC: 505 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0311 AC: 108 AN: 3468

East Asian (EAS) AF: 0.248 AC: 1282 AN: 5178

South Asian (SAS) AF: 0.104 AC: 500 AN: 4830

European-Finnish (FIN) AF: 0.0433 AC: 460 AN: 10632

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0286 AC: 1942 AN: 68004

Other (OTH) AF: 0.0303 AC: 64 AN: 2112

Alfa AF: 0.0113 Hom.: 7

Bravo AF: 0.0317

Asia WGS AF: 0.150 AC: 523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.0
DANN	Benign	0.58
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs10511866; hg19: chr9-30796759;