chr9-86760399-C-T

Variant names:

• chr9-86760399-C-T
• rs994029

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 0.703 in 152,178 control chromosomes in the GnomAD database, including 38,630 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 0.70 (38630 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.376

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.859 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: 0.703 AC: 106832 AN: 152060 Hom.: 38580 Cov.: 34

Gnomad AFR AF: 0.866

Gnomad AMI AF: 0.572

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.856

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.692

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.703 AC: 106938 AN: 152178 Hom.: 38630 Cov.: 34 AF XY: 0.706 AC XY: 52485 AN XY: 74382

Gnomad4 AFR AF: 0.866

Gnomad4 AMR AF: 0.668

Gnomad4 ASJ AF: 0.552

Gnomad4 EAS AF: 0.856

Gnomad4 SAS AF: 0.605

Gnomad4 FIN AF: 0.692

Gnomad4 NFE AF: 0.620

Gnomad4 OTH AF: 0.640

Alfa AF: 0.628 Hom.: 39018

Bravo AF: 0.712

Asia WGS AF: 0.746 AC: 2592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs994029; hg19: chr9-89375314; COSMIC: COSV68657273;