rs2094372

Variant names:

• chr9-75381543-T-G
• rs2094372

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 0.215 in 152,126 control chromosomes in the GnomAD database, including 3,719 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 0.22 (3719 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.388
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.257 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: 0.215 AC: 32706 AN: 152008 Hom.: 3719 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.215 AC: 32732 AN: 152126 Hom.: 3719 Cov.: 32 AF XY: 0.215 AC XY: 15969 AN XY: 74348

African (AFR) AF: 0.130 AC: 5419 AN: 41534

American (AMR) AF: 0.207 AC: 3166 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.264 AC: 915 AN: 3466

East Asian (EAS) AF: 0.182 AC: 941 AN: 5168

South Asian (SAS) AF: 0.245 AC: 1182 AN: 4818

European-Finnish (FIN) AF: 0.254 AC: 2687 AN: 10578

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.260 AC: 17664 AN: 67970

Other (OTH) AF: 0.228 AC: 481 AN: 2114

Alfa AF: 0.246 Hom.: 16846

Bravo AF: 0.206

Asia WGS AF: 0.250 AC: 868 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.71
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs2094372; hg19: chr9-77996459;