rs2376223

Variant names:

• chr9-32602850-A-G
• rs2376223

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 0.325 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.324 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

African (AFR) AF: 0.551 AC: 22824 AN: 41458

American (AMR) AF: 0.259 AC: 3954 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1051 AN: 3472

East Asian (EAS) AF: 0.0478 AC: 248 AN: 5184

South Asian (SAS) AF: 0.154 AC: 743 AN: 4822

European-Finnish (FIN) AF: 0.280 AC: 2970 AN: 10596

Middle Eastern (MID) AF: 0.178 AC: 52 AN: 292

European-Non Finnish (NFE) AF: 0.246 AC: 16732 AN: 68006

Other (OTH) AF: 0.271 AC: 574 AN: 2116

Alfa AF: 0.283 Hom.: 11202

Bravo AF: 0.334

Asia WGS AF: 0.128 AC: 446 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.9
DANN	Benign	0.24
PhyloP100		0.042

Splicing

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

Other links and lift over

dbSNP: rs2376223; hg19: chr9-32602848;