9-96781519-G-T

Position:

• chr9-96781519-G-T

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 0.143 in 150,948 control chromosomes in the GnomAD database, including 3,486 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 0.14 (3486 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21559 AN: 150832 Hom.: 3453 Cov.: 31

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.0198

Gnomad AMR AF: 0.0688

Gnomad ASJ AF: 0.0246

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.0956

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0164

Gnomad OTH AF: 0.0983

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

GnomAD4 genome AF: 0.143 AC: 21631 AN: 150948 Hom.: 3486 Cov.: 31 AF XY: 0.147 AC XY: 10850 AN XY: 73676

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.0686

Gnomad4 ASJ AF: 0.0246

Gnomad4 EAS AF: 0.344

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.0956

Gnomad4 NFE AF: 0.0164

Gnomad4 OTH AF: 0.0973

Alfa AF: 0.0208 Hom.: 16

Bravo AF: 0.152

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.0
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10978953; hg19: chr9-99543801;