rs2376223

chr9-32602850-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 0.325 in 152,146 control chromosomes in the GnomAD database, including 9,723 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 0.32 (9723 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.545 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: 0.324 AC: 49325 AN: 152028 Hom.: 9684 Cov.: 32

Gnomad AFR AF: 0.550

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.0475

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.191

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.325 AC: 49421 AN: 152146 Hom.: 9723 Cov.: 32 AF XY: 0.319 AC XY: 23722 AN XY: 74410

Gnomad4 AFR AF: 0.551

Gnomad4 AMR AF: 0.259

Gnomad4 ASJ AF: 0.303

Gnomad4 EAS AF: 0.0478

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.246

Gnomad4 OTH AF: 0.271

Alfa AF: 0.306 Hom.: 1033

Bravo AF: 0.334

Asia WGS AF: 0.128 AC: 446 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	3.9
Dann	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2376223; hg19: chr9-32602848;