9-76995712-T-C

Position:

• chr9-76995712-T-C

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 0.0837 in 151,452 control chromosomes in the GnomAD database, including 925 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 0.084 (925 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634

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 (EAS) allele frequency at 95% confidence interval = 0.206 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: 0.0837 AC: 12665 AN: 151334 Hom.: 925 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.00881

Gnomad AMR AF: 0.0790

Gnomad ASJ AF: 0.0413

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.0456

Gnomad FIN AF: 0.0717

Gnomad MID AF: 0.0419

Gnomad NFE AF: 0.0263

Gnomad OTH AF: 0.0659

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

GnomAD4 genome AF: 0.0837 AC: 12680 AN: 151452 Hom.: 925 Cov.: 32 AF XY: 0.0842 AC XY: 6237 AN XY: 74070

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.0789

Gnomad4 ASJ AF: 0.0413

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.0454

Gnomad4 FIN AF: 0.0717

Gnomad4 NFE AF: 0.0263

Gnomad4 OTH AF: 0.0699

Alfa AF: 0.0557 Hom.: 57

Bravo AF: 0.0888

Asia WGS AF: 0.122 AC: 423 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	2.7
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs79460104; hg19: chr9-79610628;