chr9-79424447-A-G

Variant names:

• chr9-79424447-A-G
• rs2378383

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 0.1 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
• Publications: 20 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0338 AC: 1402 AN: 41504

American (AMR) AF: 0.137 AC: 2087 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.0827 AC: 287 AN: 3470

East Asian (EAS) AF: 0.133 AC: 683 AN: 5138

South Asian (SAS) AF: 0.0967 AC: 466 AN: 4818

European-Finnish (FIN) AF: 0.193 AC: 2033 AN: 10534

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7865 AN: 67970

Other (OTH) AF: 0.101 AC: 214 AN: 2110

Alfa AF: 0.105 Hom.: 2156

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
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs2378383; hg19: chr9-82039362;