9-96781519-G-T

Variant names:

• chr9-96781519-G-T
• rs10978953

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 0.143 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.386 AC: 15875 AN: 41142

American (AMR) AF: 0.0686 AC: 1040 AN: 15168

Ashkenazi Jewish (ASJ) AF: 0.0246 AC: 85 AN: 3462

East Asian (EAS) AF: 0.344 AC: 1755 AN: 5096

South Asian (SAS) AF: 0.114 AC: 547 AN: 4782

European-Finnish (FIN) AF: 0.0956 AC: 979 AN: 10244

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0164 AC: 1113 AN: 67756

Other (OTH) AF: 0.0973 AC: 204 AN: 2096

Alfa AF: 0.0349 Hom.: 74

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
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs10978953; hg19: chr9-99543801;