rs2376223

Variant names:

• chr9-32602850-A-G
• rs2376223

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;