rs2378377

chr9-79404945-A-G

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 0.251 in 152,110 control chromosomes in the GnomAD database, including 6,365 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 0.25 (6365 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38087 AN: 151996 Hom.: 6348 Cov.: 32

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.251 AC: 38149 AN: 152110 Hom.: 6365 Cov.: 32 AF XY: 0.250 AC XY: 18572 AN XY: 74380

Gnomad4 AFR AF: 0.470

Gnomad4 AMR AF: 0.221

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.125

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.217

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.213

Alfa AF: 0.166 Hom.: 3162

Bravo AF: 0.265

Asia WGS AF: 0.170 AC: 591 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	5.8
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2378377; hg19: chr9-82019860;