rs2378592

Variant names:

• chr9-81880312-G-A
• rs2378592

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 0.211 in 152,052 control chromosomes in the GnomAD database, including 3,509 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 0.21 (3509 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32089 AN: 151934 Hom.: 3503 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.211 AC: 32111 AN: 152052 Hom.: 3509 Cov.: 32 AF XY: 0.209 AC XY: 15568 AN XY: 74324

African (AFR) AF: 0.190 AC: 7882 AN: 41486

American (AMR) AF: 0.250 AC: 3816 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 893 AN: 3468

East Asian (EAS) AF: 0.161 AC: 833 AN: 5168

South Asian (SAS) AF: 0.142 AC: 686 AN: 4818

European-Finnish (FIN) AF: 0.216 AC: 2278 AN: 10568

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.219 AC: 14857 AN: 67980

Other (OTH) AF: 0.248 AC: 525 AN: 2114

Alfa AF: 0.218 Hom.: 13392

Bravo AF: 0.216

Asia WGS AF: 0.176 AC: 609 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.50
DANN	Benign	0.66
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2378592; hg19: chr9-84495227;