9-79424447-A-G

Variant names:

• chr9-79424447-A-G
• rs2378383

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 0.1 in 151,998 control chromosomes in the GnomAD database, including 970 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 0.10 (970 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.153

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.132 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: 0.100 AC: 15215 AN: 151880 Hom.: 962 Cov.: 32

Gnomad AFR AF: 0.0338

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.0827

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.0968

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.100 AC: 15228 AN: 151998 Hom.: 970 Cov.: 32 AF XY: 0.104 AC XY: 7752 AN XY: 74282

Gnomad4 AFR AF: 0.0338

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.0827

Gnomad4 EAS AF: 0.133

Gnomad4 SAS AF: 0.0967

Gnomad4 FIN AF: 0.193

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.101

Alfa AF: 0.106 Hom.: 1472

Bravo AF: 0.0960

Asia WGS AF: 0.117 AC: 407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.8
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2378383; hg19: chr9-82039362;